Strawman, I agree with a lot of what you say, but I'm certain that of your two options for Indonesia, only one is acceptable. You may think it'd be fun to knock over their complacent and corrupt excuse for an administration, but I doubt that the resultant chaos and unchecked militancy that would succed it would make things easier for us.
As for cost-benefit analysis, I look at it like this. Not going into Iraq: the benefit is not having to fight a war. The cost, on the other hand, could be New York going up in a thermonuclear fireball. (I know that sounds a bit implausible, but so would the events of 9/11 if you'd described them to us on 9/10.) We also lose the opportunity to fix a hellish police state and throw a serious scare into the rest of the Middle East. Going in is a tough decision, but I think we gain a lot more by doing so than by hanging back, however virtuous our motives for inaction may be.