Indonesia hasn't been much involved so far; the Malaysians have been trying to act as a broker, but of course there's a fair bit of mistrust on the Philippine side, given the Sabah claim (fairly dodgy, but many Filipinos remain emotionally attached to it) and the history of Malaysian support for the MNLF in the 70s. It might be possible for Indonesia to play a role, but it's hard to see what they could do about this incident.

MANILA, Philippines—After five days of heavy fighting, Moro National Liberation Front (MNLF) Chair Nur Misuari and Defense Secretary Voltaire Gazmin have agreed to observe a ceasefire and discuss a “peaceful settlement” of the crisis in Zamboanga City, Vice President Jejomar Binay said Friday night.
Gazmin denied this soon after, and the fighting went on unabated. The Vice President belongs to the opposition party, and may have been trying to grab a bit of TV time.

CAUSES OF THE SUDDEN ERUPTION OF FILIPINO-MORO WAR IN ZAMBOANGA CITY

The Filipino-Moro war raging now in Zamboanga City between the colonial Philippine occupation soldiers and the Bangsamoro freedom fighters of the Moro National Liberation Front (MNLF) could not have occurred if the present Aquino government respected only the September 2, 1996 MNLF-OIC-GRP Jakarta Peace Agreements.
The MNLF really has only themselves to blame: after the '96 agreement they descended into factionalism and the leaders who were able to gain official positions were too busy at the feeding trough to look after the mass base, much of which splintered away to the MILF, ASG etc. Now of course the MNLF sees themselves being boxed out of the process and they want to push their way back in. While they have degraded to a large extent they still have sufficient force to make a mess, and if they get money they can raise more... sub-leaders and their troops in the region change allegiance very easily and will follow the money.

Where the money comes from is another question. There are strong suspicions that the fighting is related to events in Manila, where a huge corruption scandal has been unfolding. A number of those in the center of the scandal are core opposition members, including some figures who have been at or near the center of events for a long time. Some of these individuals are known to have been involved in coup plots in the past, some are well connected in both the military and the rebel movements.

There's suspicion that the Kiram incursion in Sabah was actually staged to embarrass Aquino (it succeeded) and diminish his hold on government (less successful), and there are suspicions that this incident in Zamboanga is a shot across the bow: lay off the untouchables or more of the same will follow.

Interesting times...