Maybe the Doctor was more afraid of trying CPR and failing? Or maybe he felt that Amy needed to deal with the moment and have the opportunity to "save" Rory's life with something that was simply human as opposed to a Deus ex machina or in this case a Docēre ex machina
Rory did drown. Maybe the Doctor has had his hands more than burnt once when he's interfered in another's life path (Waters of Mars).