Dayuhan,

I don't know if it is as bad as the author makes out, but I do agree if the peace deal goes bad it will likely lead to another surge in fighting/killing. The younger members of the MILF are not as interested in peace as the senior leaders of MILF whose time is probably short. A lot of potential spoilers on both sides of the fence.

We have to disabuse ourselves of the naive, sappy “give-peace-a-chance” mentality that peace accords always lead to the silencing of guns. From Neville Chamberlain’s 1938 Munich Agreement with Adolf Hitler, to the 1973 Paris Peace Accords that led to the fall of Saigon, to the 1995 Dayton Agreement that ended the Bosnian War but led to the “ethnic cleansing” in Kosovo, ill-conceived peace pacts in the world’s history have often led to greater hostilities. Violence after failed peace pacts intensifies as the parties claim that they were betrayed, infuriating their fighters to fierceness.
This quote, also from the article you linked to is disappointing if true:

The military brass weren’t even invited to the ceremony attended by over 100 MILF commanders. An Army general in the field lamented: “That omission struck deep in the heart of our soldiers. No credit was given for the AFP’s vital role in creating the conditions for peace talks to proceed. Mr. Aquino praised the efforts of the MILF but not the AFP, as if our soldiers were the aggressors, not the noble defenders of our land. ”
How deadly has the conflict been?

http://www.globalsecurity.org/milita.../para/milf.htm

On 07 October 2012 it was announced that the Philippine government had reached a preliminary peace agreement with the Moro Islamic Liberation Front, the country's largest Muslim rebel group, to end the four decade long insurgency that had killed more than 120,000 people.
relevant history:

Formal peace talks between the MILF and the government began in April 2004, when a peace deal was scheduled to be signed in September 2006. In 2008, when both parties were in the very last throes of hashing out a Memorandum of Agreement on Ancestral Domain (MOA-AD) agreement, the Philippine high court called some provisions unconstitutional and this sparked a rebellion within the MILF that left hundreds dead and hundreds of thousands displaced.