Anyone who has been involved in the MMO scene for a while has been around a situation like this. Even though it's just a game, sometimes temper gets the best of people. I'm sure we all have our fair share of stories.
I'm not a fan of same faction warzones for a similar reasons. I've been part of games where there's bickering among same faction members and it sucks for everyone, even if you're not directly involved. Although that tends to be more of a problem with open world PvP games.
That being said, it's a necessary evil until there are cross-server queues. It really can't work any other way. Even then there will probably still be a need for same faction warzones. Unfortunately it's just something you're going to have to deal with.