A big weakness in Quirrell's plan (assuming he wanted a successful prison break) was counting on Harry to maintain a stable Patronus. Harry is young, inexperienced at casting Patronus, and in a place liable to cause extreme emotional reactions, and he must maintain a Patronus strong enough to keep them hidden from Dementors but not so strong that it starts destroying Dementors or attracting attention.

The trouble started when Harry's escalating Patronus attracted the Aurors' attention, which was a foreseeable (and foreseen) risk. And it doesn't seem all that surprising that Harry's Patronus would go out when he saw Quirrell cast Avada Kedavra (although it is very surprising that it would block the spell).