I think delving into real religion sounds better on paper than how it would work in reality. The moment you say one religion is correct and the others are wrong, forget it. I prefer enough room so that a viewer can decide for themselves. I would not appreciate Star Trek outright favoring one religion or a particular branch of a religion over another.
I don't believe in a Supreme Being because there's always room for improvement. Thus I think it's impossible to be supreme. I do believe there's a possibility for supernatural existence and for beings that might seem godlike but aren't "supreme", but I don't think a starship would be running into them hanging out in space.
And before someone mentions TFF, that proves my point. Sybok wanted to find God and all he found was something pretending to be. Beings existing on another plane of existence wouldn't be encountered in this one. At least not physically in the same dimension.
I also don't know if a show called Discovery would really be the place to delve into something it would be impossible for anyone to truly discover in their mortal lifetimes. It's forever un-discovered to society at large or anyone living. Which actually makes it the opposite of discovery. That's why "The Undiscovered Country" literally refers to death.
Once you die, you can't exactly go back and tell everyone else about it. Because you're dead! And even if you could, you can't talk to someone about something they can't picture in their mind because they're incapable of perceiving what's beyond our ability to understand. It would be like if you could see a new primary color. It's something you could imagine but the rest of us wouldn't be able to. We wouldn't know how. Or as Spock said, "It would be impossible to discuss the subject without a common frame of reference."
If you can never truly know, then all you can have is what you believe. Without proof of something, all you can do is have faith in it.
EDIT: While we're on this subject... Six years ago, someone tried to induct me into a Masonic Lodge. He wanted me to become a Freemason. He went into the whole spiel and then, after all that, asked me, "Do you believe in a Supreme Being?" Then I said I was agnostic. Then he up and said, "Oh, then you can't join." And that was the end of that. I felt bad for him going into the whole thing before he asked me that one critical question.