If the Church of Scientology was smart, they'd try to sign some kind of mutual NDA where both Cruise and the church agree not talk about each other to anyone. Tom Cruise could potentially do some major harm to the church if he was out spoken about what Scientology is all about. I don't know what Scientology has on Tom, but if he leaves and goes from poster boy to most out spoken critic, could be really bad news for Scientology.
Unsurprisingly, they actually do that with everyone who leaves Scientology.