I tried to say this before, but apparently it got lost in my bad expression: civil war and other bad outcomes seem vastly more credible if they happen to serve Quirrell's goals. And some of them would.

He's Quirrell. Quirrell doesn't even need to snap his fingers to make that sort of thing happen. No doubt from me.

Harry's mistake doesn't lie in going against Dumbledore, I think. It lies in failing to update the probability of Quirrell indirectly killing someone to manipulate Harry, based on Azkaban.

He does seem to trust Quirrell an awful lot.