It's an interesting thought, and I'm curious-- do a lot of guilds do this already? To tell the truth, I've been kind of absent from my guild's Karazhan runs lately, but from what I've heard, we pretty much keep things separate-- Team A has their progression, and Team B has theirs. But regularly mixing up the teams seems like a good plan. Sure, with one newb on Team A, their progression might slow a little bit (and there might be a little drama coming out of forcing a certain veteran onto Team B), but by switching things up, it seems that overall both teams will benefit, and especially when you're headed for a 25 man instance (where you'll need both teams and then some), that's an ideal situation.
What's your guild like? If you have two Karazhan teams, do you mix them up periodically, or does Team A stick to themselves, and make Team B learn the bosses on their own?