You're going to get Crystal Tower most of the time regardless because it is the only Alliance raid everyone queuing for Alliance roulette is guaranteed to have unlocked, not to mention there's a high chance you're going to get matched to a player doing it for the first time for MSQ.

If you're tired of getting it, don't queue for Alliance roulette. There are plenty of XP and tomestone sources to choose from other than Alliance roulette. Direct queue for the Alliance raid you want to do if you're specifically in the mood for one.

I don't expect SE to do anything about it because it would be a complicated mess to program and they don't like to micromanage player content choices. While I think moving it to MSQ roulette would be a decent solution since it's now mandatory, I imagine because matchmaking for Alliance is different from a 4 man or 8 man there would be problems with queues.