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Katie Holmes may say her decision to divorce Tom Cruise is over Scientology, but sources close to the actor says it’s not and she’s motivated by something else.

What, they won’t say. Yet.

A source close to Cruise tells TMZ that Holmes’ camp is leaking false stories to the media claiming she’s trying to save Suri from the grips of Scientology.

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But, as the well-connected Tom source put it, “She [Katie] was totally committed.”

“She had a great enthusiasm for Scientology and would voluntarily and gladly participate in it, including when Tom was off shooting movies.”

“This is not a fight over religion. It’s being used as a way to hurt Tom.”

It’s possible, of course, that Katie was committed to it because it was important to Tom, but soured on it of late because of Suri, as reports claim.

Still, Cruise sources claim Suri is being used as a weapon against him and that his now-estranged wife is making it very hard for him to talk to her.

Tom’s lawyers have not filed anything in court – yet – to establish custodial rights. When he does, he’ll likely contest her request for sole custody.

As for what Tom’s people say the divorce is really about if it’s not really Katie’s fear of Scientology, they won’t say yet, but promise “it’s coming.”

Not vague or ominous at all.

Meanwhile, a Holmes source says that Tom Cruise controlled her like a manager or puppet master, making every major and minor decision for her.

With NO reference to Scientology this time, the source says in the end, she felt like she couldn’t breathe without his permission and had enough.