Edit: Didn't really wrap up my final thought.
Thought experiment: If the guys running Less Annoying CRM are strong atheists (note: I have no idea what their religious beliefs are), and this post was about whether or not they'd provide support for a devoutly christian customer, what would the reaction be? Would you still think it's ok for them to boot the customer because their principles don't mesh with their customer's?
Could you explicitly turn away all Christians? No. Could you turn away the Westboro Baptist Church? Yes. Morals are defined inside the law if you want to stay in business for very long.
Also, advocating or even practicing exclusivity is not a precedent as it has been going on for centuries, in thousands of different forms.
Some of those most people disagree (e.g. there was a time a black man would not be served in many restaurants) and some of those people accept as completely valid (e.g. I'm sure there are many country clubs I'm not eligible to join).
Just don't complain when all the religious customers go away.
Note, this actually happened, and people were outraged. http://freethinker.co.uk/2011/11/23/missouri-ice-cream-shop-...
Another thing to consider, this guy that banned athiests, why not ban ALL other religions? Seems a bit hypocritical, but still, it's up to him.
(Yes I'm aware that religious discrimination is illegal.)