1. If the company makes allowances for any reason then they have shown it is acceptable. It's not the reason for the exemption, but the cost. If the they can bear the cost for someone's medical problem, they can bear it to comply with the 1964 civil rights act.

2. "Congress shall make no law respecting an establishment of religion." State religion is banned by the first amendment. End of story. A court cannot say what is and what is not an acceptable religion. It cannot say which beliefs are reasonable and which are not. Again, the only thing that matters is at what point the cost of an accomodation becomes unreasonable for the company.