I think it’s really up to you. Since sci-fi tends to be more secular than fantasy, I think putting any kind of god-figure in it would be interesting and unique. If you have different alien races, I’d definitely think about the god’s/gods’ plan for them and how they relate to the god(s), just like you would if you were writing fantasy.
"For He knows our frame; He remembers that we are dust." - Psalm 103:14