conflict with an affiliate of a publisher?

I don't think anyone here could predict that. I would suggest discussing it with the convention folk you know and asking them. In my experience, being open about and knowing about things in advance gives people their best chance to take the high road. Whether they do or not, you should do what you think is best for the book/your career.

As veinglory said, this is hard to predict - and I'm a conrunner. As she said, be honest about it. Give your home con the opportunity to deal with it now. Might there be someone on their board or high level staff who might be sympathetic to your situation? That might be a place to start.

I hope it works out for you - both the publication and the convention situtation

I realise that this is a tricky situation (loyalty is a big deal - trust me, I know), but don't let politics hold back your career. Especially politics that you are technically not involved in. YOU aren't the one in the fight with that convention, your friends are. Now, if that other convention is in a fight with the people you are friends with because they have amoral practices, well that's one thing. You might want to seriously consider not going with a publisher who has such tendencies. But if it's a matter of a con battle over guests, space etc. Then I would say do what's best for you.

Why should you sacrifice your writing career because other people can't get along?

ETA: And I think any publisher that would forbid you from doing other events that would not only benefit you but that publisher (like selling books published by them at your friends' convention) is not a publisher I think you want to work with. And any friends who wouldn't allow you to further your career by going with a legit publisher and supporting you at their convention aren't really good friends.

But I realise that that is oh so easy for me to say. Like the others have said, communication is key to all this. But quite honestly I'm pretty annoyed for you that you aren't allowed to pursue your dreams because of someone else's battle.

Cart before the horse. Your book hasn't been accepted yet. This may never be a problem.

Given what seems to be various relationships at play, word might get out the second she does submit.

Decide what you want to be: An author or a con-runner.

If it was a big publisher, the idea of them wading into a schoolyard-style dramafest would be a bit boggling. So though I'd agree with the general sentiment that someone else's battle shouldn't hold back your career, the whole situation sounds very small. I'd question if the publisher is really going to help your career, before you sign up for the drama.

If I'm wrong and it's an imprint of Random House (or similar), you really have nothing to worry about. They won't be personally invested in the things they sponsor. Not in the sort of way where they'd want to get involved in a feud between conrunners.