sorry, but I really think the time has come to confront her. you don't have to do it on your own, but don't overwhelm her (I'm assuming she's getting on a bit).
she can't be trying to turn your son against you, no matter what she's using as an excuse. you wouldn't take that from anyone else, so you mustn't take it from her.
give her a chance to pull herself together otherwise, I'd keep him away until he's old enough to choose whether he wants to see her, based on the facts.