That's the problem. McGonagall's Patronus visited before they activated the Time-Turner the first time, because according to Quirrell's plan, all the events of Ch. 52-58 are taking place within one time-turn.

ETA: oh, sorry, I see what you mean. Maybe you're right. Maybe the allotted time ran out during Ch. 55, thus saving them by pure chance. Then Eliezer only needs to change Quirrell's phrase in Ch. 58 saying "original plan carries on undisturbed". On further reflection, this would've been be a smart plan from the start: if you have an unrestricted Time-Turner, you can carry out complicated plots in the future. Go back by 2 hours, escape the room, wait 3 hours unseen, do your job, go back by arbitrary amount. Like Ocean's Eleven in reverse.