If you and your chlidren's beliefs in their own religion were strong enough, I think a simple movie --- one that might make them think about religion (whether that thought is positive or negative --- wouldn't be "harmful". If someone changes their mind and decides that they don't really believe in God anymore, or follow their religion so tightly, then that's their choice, isn't it?
By saying this movie is anti-Christian and boycotting it, the thing Catholics seem most afraid of is the fact that it may make them or their children "think" and see the viewpoint of another religion (assuming Atheism is a form of religion, as it is, in itself, a belief). Or what if their children don't grow up Catholic? Oh my goodness.....that would mean none of the religious "training" worked! By learning about many different viewpoints, they may not choose to be Catholic, so its best to limit their exposure to all anti-religious things and only allow them to watch movies like Passion of the Christ. It's not brainwashing or anything. It's just that "my children
WILL grow up to be good Christians, goddamn it!"