Quirrell's case in favor of Bellatrix's innocence sounds like what a partisan would say when trying to make their side seem favorable, not an argument that Harry would buy (just as he could see through Draco's case against Dumbledore). Genre savvy Harry has read plenty of stories about villains with a sympathetic backstory.

This is the one thing that bothers me about this; Quirrell's excuse for Bellatrix seems good enough to cover a lot of people. Hence I expect at least one of the following should hold:

• Harry refuses to go along (this didn't occur)
• Harry insists on modifying the plot to break out more people (this didn't occur)
• Harry insists on going back to break out more people, to Quirrell's dismay
• Harry insists on going back to break out more people, just as Quirrell was going for

...though I guess those last two look a good deal less likely now that I've seen the extent to which they bungled the breakout.