I think that McGonagall has learnt enough to be suspicious of Harry, but she's still more circumspect than to call him on it in front of the whole school. Maybe she'll check up a bit later, and maybe in private Harry will be happy to tell her the truth anyway, with appropriate precautions. On the other hand, if he's decided not to tell her, then he'll arrange not to be found until it's too late. (When is it too late to check if a time turner has been used?)