Okay, if you want to play with flawed comparisons, what if there were a ban on the stoning to death of women for such crimes as cohabitation with another man? Should we pity this poor, abused religious community for having their rights infringed?
The comparison you are making here is indeed flawed. Circumcision is an essential aspect of both Judaism and Islam, while the stoning to death of people isn't. Circumcision is a religious ritual, while stoning is a form of punishment. It is a condemnable practice and is, sadly, still practiced by extremists, but in no way is it on par with circumcision when it comes to its significance for Jews and Muslims.
Any religious practice which actually harms people in a clearly tangible way should obviously not be legal. But that's not the case with circumcision; there is no proof that it harms those who are involved. On the contrary, the example of millions of people who are circumcised and don't care and the lack of a clear scientific answer to the question whether circumcision is positive or negative show that circumcision is a harmless practice.