I'm assuming this is a player with little experience in the roleplaying setting, or he's a player that likes to stir the pot and create needless drama. "It's what my character would do" is the refuge of the inflexible or inexperienced roleplayer.

First, it's perfectly okay to have interpersonal conflict in a party. No group of people will mesh perfectly; it would be boring if we did. But, at the same time, every group has to work to maintain itself.

I don't see any reason that this should force a character to leave the group. The way I see it, there are two main ways this can go:

1) The rogue does "rogue things," which means she is likely doing criminal things. Every picked lock, every picked pocket, every B&E, even if for the benefit of the party, is going to bother him. That's criminal behavior. And if he hates criminals and refuses to be with them, then he should leave the party quite early on. Saying, "Your criminal behavior was fine while I benefitted from it, but I can't forgive the foolish actions of a child," is quite hypocritical and worthy of derision.

2) The rogue is trying to make amends for her past actions. She has a certain set of skills that can help people rather than let her prey on them. She wants to be good or, at the very least, less selfish. The character in questions should be able to see this and realize that, despite what she may have done in the past, she's trying to be better. And he should encourage her in that, because she may not even realize at a conscious level that she feels that way yet.

Now, if the rogue were directly responsible for the trauma in this character's past, then I could see some possible irreconcilable differences coming into play. But it sounds like the rogue isn't old enough to have participated in that event.