The way I see it, MJ blowing her top is strictly Mephisto-influenced. Normally, she is the soul of understanding when it comes to this sort of stuff - she's long since come to terms with the fact that this is who her husband is and what he does, and she can no more change that than fly to the moon. I mean, the argument itself is perfectly understandable, just not the fact that it's coming from MJ. She knows that Peter loves her and would never want to hurt her, and that if he hasn't contacted her, it's because he can't. As at least one novelization has shown, MJ puts so much effort into being calm and understanding for the sake of her husband that when she DOES flip out, A: it's usually at someone else, and B: it's truly impressive. My guess is that Mephisto sparked a flash of anger in her brain at exactly the wrong time, ultimately causing their breakup. Otherwise, MJ is REALLY out of character here, is all I can say.