Whether Punk is on the roster or not, I'm expecting AJ to drop her title at or around WrestleMania XXX. AJ is the longest reigning female champion WWE has had in more than 20 years and has beaten or probably will beat anyone currently on the WWE roster that's worth watching wrestle against her. Emma, from NXT, has been shown on camera a few times lately and she's been working some dark matches, so she'll probably be wrestling on television before too long as will Paige. I'd say one of these women has a good shot of ending AJ's run as Divas Champion.
As far as WWE sort of punishing AJ over the CM Punk business, it's possible. Numerous reports say that Vince can be spiteful and stubborn. AJ probably would have been punished during the misunderstanding that happened at Tribute to the Troops had it not been for Punk exerting some influence and all parties explaining the misunderstanding. Like anyone else, Vince can let stubborn pride & ego get in the way of what makes sense.
However, in a lot of ways, Triple H has been something of a calming influence on Vince. Remember when Bryan's match against Orton was stopped on Raw because there was suspicion that he'd been injured? Reportedly, Bryan went off on Trips backstage for doing it, but they talked things out and while Vince, reportedly, suggested that Bryan be punished, Triple H talked him out of it because he understood where Bryan was coming from, as he's been in the same spot himself. No disrespect was intended, it was just a case of concern and misunderstanding. Being a wrestler himself gives Trips a perspective that Vince simply doesn't have. Because of that, I think there's a good chance that AJ won't be punished, nor should she be, for something that's supposed to have been resolved. She shouldn't be used as a scapegoat for management to take its frustrations out on because of the Punk situation. The entire women's division in WWE would fall apart without AJ. A lot of the Divas have improved quite a bit inside the ring, but AJ is, hands down, the most interesting woman WWE's had on the roster in quite some time. She's easily the most popular of the Divas, even though she's a heel, and the little girl works her ass off.
However, if AJ's smart, she'll keep her mouth shut when it comes to this whole situation. If she's asked what she thinks by someone backstage, I think the best thing she can do is say that whatever's going on is between Punk & management and that she hopes that everything can be worked out. Also, if AJ was to leave WWE because of Punk leaving...well...there's a very good possibility that AJ would be throwing away a long, promising career that eventually sets her up financially for the rest of her life. Not to put Punk down or anything, but the guy's got something of a reputation as a man ****e. He's reported to have had flings & relationships with half the women who've been on the roster for the past 10 years and there's no telling how many ring rats he's hooked up with over the years. Of course, I don't know how deep or serious their relationship is, it's just that, going by past reputation, I'm just not sure how committed of a guy CM Punk is. AJ's living her dream right now, that's something that most people don't really get the opportunity to do, so quitting WWE because her boyfriend has, supposedly, quit just doesn't seem like a smart move.
No way she gives this up, and I don't think even Punk is selfish enough to encourage her to do that. (That's not an attack on Punk by the way). Probably warning her to watch her back though.