To be fair, I believe that was Van Lente's intention. The way she's written, Mary Jane's hang-up is that she feels under-appreciated and wants more out of her life, whether it comes to her career or her relationships, especially the one she had with Peter. From her perspective, he placed more value on being Spider-Man than he did her. However, the incident involving Carr and the White Rabbit and what Carr says to her afterwards makes her realize that SHE was the one who was truly selfish in the relationship, not Peter, and rather than moving on with her life and not wanting to fall into the role of being "just the girl," she realized she running away and becoming someone she really didn't want to be. The scene after this one shows Carr trying to come up with a cover story with MJ to cover his own ass and in the conversation (along with Carr telling her giving her a variation of "Honey, you know I love you, so don't take this the wrong way but you're getting too old to be successful"--yeah, your guess is as good as mine what she saw in this douche) there's a point where he says his therapist talked about how "there's always tension in a relationship when one partner is so much more successful than the other" and the narration is over a picture of MJ's flashback to Spider-Man, with the next page followed by a close-up of MJ's face that suggest a kind of revelation.
Even so, you can tell that in order to make Peter and MJ's break-up plausible, Marvel had to seriously regress her character, as JMS pretty much tackled and resolved MJ's hang-ups over feeling second best when it came to Peter's life as Spider-Man in ASM #50 volume 2.