That doesn't make it any better, considering that it's still inherently unsafe (as the article notes and the whole reason for the law.)
It actually does. Although this particular practice is still pretty, uh, unnerving seems like a good word to use here, any situation you could name obviously is made better by subtracting sexual interest in infants.
In this situation it clearly makes a big difference as it's akin to the difference between getting a physical examination of your private parts or getting sexually abused. The difference is in the presence or lack of sexual interest when you do the action.
Just considering this scenario, I think the judge made the right decision here. While there is a right to religious freedom, this doesn't actually restrict that freedom at all, just requires parental consent for something that is... well... revolting. Parents ought to know if this is being done to their child and ought to have a say in the matter.