When I was Suri's age, I used to see my aunts and uncles more than she sees her father. The "growing up before his eyes" part -- that's the problem. She's growing up NOT before his eyes. Every time he sees her she's grown more, because he doesn't see her very often.
Scientology was certainly a problem for Katie, especially in regard to Suri -- maybe even a major problem -- but I bet there were many other problems with Tom also.
It's hard for me to believe Tom is being guided by Miscavige on how to behave toward his daughter. I think Tom himself, is probably pissed that he has to be a visitor of his own child, and is not able to mold her into the clam he would like her to be. I bet it infuriates and frustrates him to the point where he's postulating that as Suri gets older, she'll rebel and come back to him at some point. He'll be waiting with open cans.
He'd let her do anything, as long as she agrees to become a clam. This scenario is predicated on a few factors though. Katie may be a great mother, and Suri could have picked up on that Daddy was too busy and important for her, and driven by things she had no interest in. If Suri and Katie grow up bonded with a lot of love for each other, then Suri won't run to be with Daddy.
If he wants to see her in ballet, he could order a video made and sent to him, since it seems it's mostly a Skype/phone relationship anyway.
I don't think Tom would talk about anything having to do with Suri with anyone where there was a risk of it getting out. If Suri told Katie something about Daddy regretting spending more time with her, I don't see why Katie would tell anyone that.
One call from his daughter is not going to break through years of brainwashing.
