I don't think that's a fair analysis of the characters as the story progresses (except maybe for Ron, but who likes Ron anyway?) How far into HPMOR did you get?
(Something about trying to avoid dying I think)
As for the other characters, their level of agency varies, but at the very least Quirrel, Hermione and Draco are also agents (i.e. smart enough to be capable of driving the story in a meaningful way), and the other characters are portrayed fairly accurately given their stupidity in the original books.
In the original book, ALL the characters are stupid. In HP:MoR, 5 characters are not stupid. I think that's an improvement.