do not antropomorphize companies, it does not compute at all.
The group version of this right would be the Church of Christ, Scientist not needing to provide healthcare to its workers (not all of whom may be Christian Scientists themselves), in order to protect their deeply-held beliefs.
It requires specific religious protection if you're afraid of countries that persecute specific religions and want to take every measure to avoid becoming one. The Pilgrims came to America because of religious persecution. England still has a state church to this day.
I guess what I'm saying sort of agrees with you, but that I'm seeing how "clash with the values of the community at large" could refer to "have any religion except the official one" or even "have a religion". There's a possibility that the community at large could become hostile to many or even all religions in the future.
Like unions?
There is no logic in this sentence. An organised group as an entity doesn't need to be treated the same as a citizen for the freedoms of the members of the group to be respected, I don't understand where is the leap between: rights of a citizen should be extended as rights of a virtual entity that groups citizens. Why?