Actually, the Scientologists are known for physical threats against people who leave them, and also for threatening their families.
That said, the whole essence of Scientology is brainwashing, and the people who have gone through their system lose all contact with the outside world and outside realities and are completely controlled by Scientology.
Scientologists were involved in the death of Terri Schiavo, partly because her husband was involved with them and partly because the entire municipal and local government of the Tampa-St Pete area is filled with Scientologists or bought off by them. So I can see why she would be afraid to seek help from the outside, because even that could be corrupted.
Now, it all makes sense why Katie Holmes left Tom Cruise so abruptly, and also why she wanted sole custody of Suri.