It illustrates the point of staying away from present-day religion in Trek, mostly because mention of it will annoy somebody.
I'm an atheist, and I couldn't care less what someone's religion is depicted as. It's a part of culture, and different religions exist. It lends a verisimilitude to Trek that I rather enjoy.
There are many things that will annoy many different groups of people the world over. Should writers stay away from any topic for fear that some segment of the readership will be "annoyed"? I don't know about you, but to me that sounds like it would be some pretty drab prose.