Typically these issues are not addressed, because nobody in power wants to touch them. Again, there is very little the US can do to address this. It's not our fight.
You're correct in my opinion, we have little leverage to push the Gov of the Philippines to change at the local and national level, and the locals in the Muslim south very well know that the acts of kindness they benefit from are "mostly" driven by the U.S., and if we weren't there it is unlikely that the military would reach out to the locals.

This isn't our fight, and much like other efforts we get involved in we find it difficult to extract ourselves from these activities. Our military involvement in the Philippines is small relative to Iraq and Afghanistan, and perhaps affordable, so the real question then is should it be sustained?

With the current President of the Philippines I think it is worth having a little more patience to see if he can push his promised reforms through, but to date he has not yet demonstrated that he has the leadership ability of Magsaysay, and doesn't yet appear capable of pushing his reform agenda through to completion. However, he does seem to have a good vision, one that we should support in my view. Of course it is the Philippines, and it may turn out he is as corrupt as everyone else.