Off the top of my head...
1. Who is to say that NuBSG isn't about a real God? Something is guiding everything. Until we see the end of the series there is still that option. Not that I think it's really God but the option is open, isn't it?
2. Can fantasy be classified as SciFi? It seems that way when I go to the video store. Therefore movies/shows like Clash of the Titans, Xena, Hercules all fit the request.
3. Are you limiting yourself to movies or TV? If not then I suggest you read Heinlin's "JOB: A Comedy of Justice" Heaven, Hell, God, St. Peter... all presented as real characters and not super powerful aliens. I've not read any of Piers Anthony but my impression is his books fit as well.
4. Time Bandits. OK, God isn't a major character and isn't presented as an all powerful being. On the other hand, it still fits your request. Good vs. Evil. God vs. Evil.
5. Are you really looking for a movie like "Oh God" or "The Ten Commandments" just in a futuristic setting? Would the "Left Behind" series of books (and straight to video DVDs with Kirk Cameron) fit in this category?
I'm guessing it boils down to what you call science fiction. If I write a story set in the year 2009 or 2010, is it science fiction? It's about the near future, after all. Perhaps speculative fiction would be a better title.
As has already been belabored for six pages now, it appears you're looking for science fiction that fits your personal nitch of belief. That's fine. Many may get upset with you about this but hey, equal time for opposing views, no? Why is it OK for science fiction to cater to the atheist or agnostic but not the true believer?
Of course, you need to be willing to accept stories where a Jewish God or Hindu Pantheon or Muslim God is the ultimate universal being (or beings). Perhaps there are. I referred to the "Left Behind" series above. That fits with Christendom's POV. I'm not familiar enough with other cultures to know if their literature also have similar stories/authors.
What is science fiction? Would a story about the Crusades be science fiction? What if you take the story of the Crusades and set it in the far future (or a long time ago

) with lightsabers instead of swords? Is changing the tech level or planetary location enough to make it science fiction or is that just window dressing?
As a side note - Someone mentioned something about God "needing" worshipers. That's not correct. God doesn't "need" worshipers. He doesn't need anything.