Some peace is not worth it. A state that suppresses its citizens and others does not deserve peace for such peace only allows the state to continue to use its power to bully. Peace is sustainable only if rights are respected. No peace can stand with disrespect.
For other peace, it is worth the shot and it should be welcomed. One of such peace is the one almost everybody is shooting for in Mindanao. It is worth the shot because I do not think the government of Philippines is one comparable to that of Saddam Hussien of Iraq or al-Assad of Syria. Furthermore, the conflict has been going on for a long time much to the disadvantage of everybody in the Philippines, and possibly to Malaysia as well although arguably, Malaysia did benefit from the conflict given the context of the formation of Malaysia and the Filipino claim to Sabah in the early age of modern nation-states in Southeast Asia. The conflict in Mindanao essentially distracted the government of the Philippines from pursuing its claim more vigorously. Also, Malaysia, both the state and private citizens, had been naughty with respect to Mindanao in the past, just as they had with Aceh.
But that does not mean that there is no cost to Malaysia. Security in eastern Sabah had attracted attention in the past. The US government has issued travel warnings from time to time, which I think can be an unfair representation of Malaysia as a whole which is very safely relative to most neighboring countries. There have been several high-profile kidnapping cases in the past and this has caused the military to beef up its presence in that area. Whereas Malaysia could spend its resources on building up public infrastructure in Sabah, which is severely lacking compared to Peninsular Malaysia, the same resources went to security purposes. The security spending is necessary but it would have been great if it was not.
Another cost, which is bigger, has been illegal immigration into Sabah. I personally prefer assimilation for these immigrants because they have been here for such a long time. The cost of assimilation should be reasonably cheap compared to mass expulsion. I also think expulsion is an inhumane policy. I think we have a responsibility to welcome these immigrants as long as they are willing to work and become good residents. It is cruel to force them back in harm’s way.
But the politics in Sabah is murky and assimilation that a libertarian like me prefers is not a popular proposal among Sabahans. Some Sabahans hold almost racist (outright racist even?) view when it comes to the issue. So peace is one way which the problem of illegal immigration can be solved, even partially.
Peace is Mindanao may encourage some refugees to return home. Peace also may finally allow for economic development on the island and that may encourage economic migrants in Sabah to return home as well. Peace itself will encourage greater trade between Mindanao and the surrounding regions and that has to be good for Sabah and Malaysia.
But it is still to be seen if there will be peace in Mindanao despite the fanfare. A wholesome peace requires that the rebels are represented wholly and already there are fractions opposing the proposed deal. One hopes the rebelling fractions are only a minority, unpopular and unarmed. Unfortunately, it is quite clear that they are armed. Besides, how many broken peace deals were made in the past?
I also wonder though how will the effort at peace there will affect the Filipino claim to Sabah.