I would lay the real cause on the almighty dollar. Cruise had a contract for about 25% of gross on his pictures...practically the last such plush contract in Hollywood. The stated cause of "behavior" may have been partially as an excuse to kill this bad deal.
Even if they made moderate amounts of money (like MI3 at about 120m gross), when you subtract the high production cost + babyboys big cut, the Studio finishes upside down.
They also said the public distaste for his offscreen wierdness may have cost that last flick out of about 150m lost gross (which most analysts say is kind of an inflated number, BTW - but who knows?).
Mostly though, they probably just wanted out of a bad monetary deal that is getting more and more embarrasing. Probably not an anti-Scientology thing.
Tomkat himself whined that he could not have gotten fired, because he quit first. Waaaah!