As with all freedoms, the freedom of conscience and the freedom of religion are not infinite. For example, freedom of speech does not cover defamation. We have to acknowledge that there must be some limits placed upon religious expression. Conversely, we must also recognize that since religious beliefs are central to many people’s lives, that freedom should only be abrogated at great need.
In the case you have given — a Muslim man beating his wife under the guise of freedom of religion — we recognize that his wife’s right to safety is important enough to restrict his religious expression. This can’t be said about many of the cases surrounding religious freedom that are currently being discussed in american society. In the case of the Christian bakers, or the case of the HHS mandate, we find that we are violating an individual’s religious freedoms for relatively trivial matters. In the former case, the worst that said couple would have to do is find a new baker. I’m sure they were upset with the baker, and I’m sure that finding another baker would have been an inconvenience, but I’m not sure that the need to have people free from becoming upset or from having to find another wedding baker justifies violating a person’s religious freedom. Similarly, the consequences of having Catholic organization not have to pay for contraceptives are relatively minor. Individuals who choose to work for those organizations do will not have their contraceptives covered. I’m not sure that the added expense and inconvenience justifies violating a person’s deeply held belief.
In other words, we accept that freedom of conscience and freedom of religion have limitations, but we must also acknowledge that those limitations should be applied sparingly since the religion is such an integral part of some people’s lives.