I think your point is a good one. However, I don't think you're disagreeing with the main point of the post, since 'flawed heuristics' are more an example of the traditional 'biases' studied by researchers, which aaronsw is indeed claiming aren't that important for improving general rationality. The "not getting around to reading a 'nonprofits for dummies' book" isn't an example of overcoming a heuristic and becoming dumber, it's an example of having a knowledge/common sense gap and not applying any kind of heuristic at all. "Always read the relevant 'for dummies' book first if you want to start working on a project" is a heuristic, which is probably biased in itself, but which most people don't follow when they would be better off following it.

Also, I think there is more subtlety to 'overcoming bias' than just not using that heuristic anymore (and maybe being dumber). Heuristics exist because they are useful in most circumstances, but they occasionally fail massively when subjected to new and unexpected types of situations. Realizing that thinking happens in the form of heuristics, and then trying to notice when you're in a situation where you wouldn't expect the heuristic to apply, can help with the problem of being overconfident on a given problem. Recognized ignorance is preferable to being very certain of an answer that is likely wrong, in terms of not making decisions that will blow up in your face.