Since... well, forever. Pick up a history book covering any tumultous time and place in the world.
I'm not saying that makes it okay - just the opposite. Until more people realize that these things happen a lot, have happened, and continue to happen, they'll never stop.
As for destroying Sabaya, it's not as straightforward as you make it sound. The Abu Sayyaf is not a regular army or a regular political group - there are no central points to attack. The Philippine jungle is very large and nasty nasty nasty. Anyone with some jungle savvy who doesn't want to be found, probably won't be found. Think USA vs. Viet Nam, or USSR vs. Afganistan. Guerilla tactics are scary and effective - that's why there have always been guerillas down thru history.
So what, should everyone just give up? Of course not. But sending a bunch of soldiers to wander the jungle isn't going to do it either. The situation is much more complicated than that.