I was a guild leader during TBC, and let me tell ya, Karazhan made the conversion from 40 to 25 very difficult. Servers completely transformed.
Our guild struggled because no matter how I shuffled up players, there was an A-Team instantly. Was a lot of drama. We survived well, but so many other guilds didn't.
I don't think this will be too tough. Healthy guilds with good leadership will survive. Cliques will die. That's going to be healthy for the game