I don't see why the rise of science and advanced technology would make everyone atheist. You can be religious and believe in science at the same time. I think that a lot of what we observe in the universe even supports the concept of God, such as the Big Bang. I don't see how proof of the Universe exploding into existence is fundamentally any different from "And God said, let there be light, and there was light, and God saw that the light was good, and separated the light from the darkness." which to me sounds very much like the Big Bang and the formation of the first stars.
Also, in canon the Federation is a religiously tolerant entity. Which is why Rigelians and Bajorans are members of the Federation, as well as numerous other races with their own religious beliefs. I don't see how a chapel on ESD or on planet Earth would break canon at all.
But I personally don't care if they add it or not. There are much, much better places to seek spirituality than in a video game. What, exactly, does going to church with your STO avatar do for your immortal soul? It's presence would only serve to antagonize the other non-religious players.
There are times and places to pick your battles, and right ways and wrong ways to bring in converts. This would be the wrong place and the wrong way. Blind fanaticism only serves to drive other people away from the faith. Read 2 Samuel, Chapter 12 when Nathan rebukes King David. He could have been a douche and told David to his face that he was a murderer, adulterer, and filthy sinner. Instead he used a parable that brought to light what he did without offending him. So instead of the chapter ending with the King executing a prophet, the King is brought unto repentance. It's the same concept.
So yes, while I agree a chapel on ESD would be nice in some ways, if it ends up breeding antagonism and resentment throughout the community (which is the most likely scenario) it doesn't have any place being there.