Why was it necessary to use military methods to secede, while IRW, alliances and unions come and go, sometimes, peacefully. Does the Republic not allow a system or planet to leave and declare itself independent?

Or was it simply a pretense to wage war on The Republic?

Canon answers are prefered, but any sourced information will do.

Alliances may come and go in the real world, but secession (that is, establishing autonomy separate from the recognised government) is usually illegal. The most famous secession resulting in the American Civil War, but there have been many other attempts - some successful, and some not so - almost all have involved fighting to some degree.

The Republic is not an alliance of planets - it is a federated government. Planets and systems have some level of self-governance (like states within the USA or Australia, or cantons in Switzerland), but abide by the Law of the Republic.

Unfortunately, there isn't a lot of direct evidence about the specifics of the Republic's constitution. But the Senate is described as the "government", which implies the Republic to be a single state rather than an alliance.

The deterioration and civil war were also fomented by the Sith, which muddied things too. Considering the first shots of the Clone Wars came from the Republic against the Separatists on Geonosis (albeit to rescue a couple of foolish Jedi and a Senator), an argument could also be made that the Separatists were defending themselves.

In Earth politics it may be possible to leave an alliance unilaterally. Most treaties of alliance have clauses describing the conditions for leaving the alliance, usually giving each party the power to leave the alliance unilaterally within a certain period after giving notice of their intention.

But the Galactic Republic in Star Wars is much more similar to an independent state on modern Earth than to an alliance like, for example, Nato.

The Star Wars Galactic Republic seems to resemble a federal state or federation, in which power is shared or divided between the central federal government and the governments of the various parts of the state, but which is legally a single independent and sovereign government in international affairs.

A federation (also known as a federal state) is a political entity characterized by a union of partially self-governing provinces, states, or other regions under a central federal government (federalism). In a federation, the self-governing status of the component states, as well as the division of power between them and the central government, is typically constitutionally entrenched and may not be altered by a unilateral decision of either party, the states or the federal political body. Alternatively, federation is a form of government in which sovereign power is formally divided between a central authority and a number of constituent regions so that each region retains some degree of control over its internal affairs. It is often argued that federal states where the central government has the constitutional authority to suspend a constituent state's government by invoking gross mismanagement or civil unrest, or to adopt national legislation that overrides or infringe on the constituent states' powers by invoking the central government's constitutional authority to ensure "peace and good government" or to implement obligations contracted under an international treaty, are not truly federal states.

At the present time there are 27 federations or federal states listed out of approximately 195 independent states in the world. Most of the largest and/or most populous nations are federations.

Most sovereign states are unitary states with a single government for the whole state.

A unitary state is sometimes one with only a single, centralised, national tier of government. However, unitary states often also include one or more self-governing regions. The difference between a federation and this kind of unitary state is that in a unitary state the autonomous status of self-governing regions exists by the sufferance of the central government, and may be unilaterally revoked.

Another type of state is a confederation.

A confederation, in modern political terms, is usually limited to a permanent union of sovereign states for common action in relation to other states. The closest entity in the world to a confederation at this time is the European Union. While the word "confederation" was officially used when the present Canadian federal system was established in 1868, the term refers only to the process and not the resulting state since Canadian provinces are not sovereign and do not claim to be. In the case of Switzerland, while the country is still known as the Swiss Confederation (Confoederatio Helvetica, Confédération suisse) this is also now a misnomer since the Swiss cantons lost their sovereign status in 1848.

If the Galactic Republic in Star Wars was a confederation of independent and sovereign states for common action with regard to other sovereign states then each of the planetary, star system, or interstellar governments which joined the Galactic Republic would have the right to unilaterally withdraw from the Galactic Republic and there would be an official procedure to do so. Therefore it would be unlikely for separatists to risk civil war by illegally seceding instead of by seceding by the legal method.

The only confederation existing at the present is the European Union, and it is legally possible for a member nation to unilaterally withdraw from the European Union, as the United Kingdom is doing now via "Brexit".

Therefore, I deduce that the government of the Galactic Republic has no legal method for planetary, star system, or interstellar, governments to secede from it. Therefore, the government of the Galactic Republic should resemble either a federation or a unitary state (perhaps one with a lot of autonomy for member governments) instead of a confederation.

Note that the Galactic government is not called the Galactic Union, the Galactic League, the Galactic Confederation, or the Galactic Federation, but the Galactic Republic. Thus there is nothing in the name of the state to indicate whether is is a unitary state, a federation, or confederation.

The Republic was not an alliance. It was not a trade union. Membership in the Republic was not voluntary, not optional. While its self-characterization as the "Galactic" Republic was overly optimistic, with certain functionally independent areas on its fringes and other parts of the galaxy remaining unknown because they had never discovered a safe hyperspace route into them, the Republic claimed the entire known galaxy because only by being the only interstellar nation could it avoid interstellar warfare and the need to maintain a large military to be ready for it.

If they had just let the Confederation go without a fight...what would have happened next? Would the two megastates just have lived alongside each other in relative amity with any issues resolved by diplomacy? Of course they bloody well wouldn't have. You only had to look at the Trade Federation's attempt to secure a trade monopoly on Naboo by force to know that wasn't how it was going to go. There would be wars between the Republic and the Confederation. And in between the wars the Republic would have to maintain a large standing military all the time and tax its members accordingly.

Now of course there's a flaw in this reasoning. Notably that there was a very real possibility that some day the Republic would face an invasion from the Unknown Regions or another galaxy and be totally unprepared for it. However balanced against that theoretical risk was the probability that the Republic would get enough forewarning of this new element in time to respond and the actuality that the Republic had gone for a full thousand years without any significant interstellar warfare. So win this civil war and they could in theory hope for another thousand years of peace and almost no Republic taxes.

Not a full canon answer, but at least an attempt of an in-universe explanation:

A point made in this video by EckhartsLadder is that although peaceful secession WAS legal, in many cases the CIS (manipulated by Darth Sidious) was not properly representing the nations willing to secede. To summarize: a small group of citizens (eg: corrupt government, or a party in a local civil conflict) influenced by the CIS makes an illegitimate claim for secession without proper public support (eg. public vote), while the majority does not support this, or are even unaware. Finally that majority calls the Republic for help. The Republic has to take action, because it is obliged to help own citizens.

The author claims that a full canon answer cannot be given, because a text or at least a quote of the Galactic Republic Constitution, that governs this matter, was never published.

Palpatine is the one also working with the Separatists. Why would he actually help them if what he wants is to cause strife to take over as Emperor? Darth Sidious never intended to actually help the Separatists. Probably while he works in the shadows with them in the Galactic Senate he probably is making stronger rules and regulations on how a planet could leave the Republic. Or shutting down actions that could lead to actual separation. Palpatine wanted the chaos that possible session can cause (look at all the independence movements in Earth's history, or how even modern attempts like the cases said above of Cataluña and Scotland. I mean where I live they have tried time after time to get people to agree on a status resolution and one of the latest plesbicites was nulled because the definitions of the options where not clear enough).