Any desire to retreat to science fiction as some kind of "religion free" zone is seeking to put some kind of artificial barrier, some kind of sanction on the storytelling that is simply unnecessary and does not at all reflect on the human experience.
What I want to know is why some science fiction fans feel the need to recoil at the idea that some DO take seriously the idea of diety/spirit/what have you.
I think it should be pointed out that writing about
religion is not the same thing as writing about
divinity. Religion is a human institution revolving around the belief in divine entities or forces that shape our lives. It's certainly possible to write about a religion, i.e. a cultural institution, without postulating the reality of the things it believes in. So a science fiction story dealing with an alien religion or belief system is merely engaged in sociological speculation and worldbuilding, exploring what it is the alien society believes and how that belief affects their behavior and their lives. There's certainly no need to manifest those beliefs as concrete realities.
Alternatively, one can depict an alien religion built around something that has a secular, scientific explanation, as was done in
Stargate and DS9 (though DS9 was a little more ambivalent about it toward the end). Again, just because the story depicts characters believing in something, that doesn't mean it's treated as objectively real (at least in the sense they believe) within the story.
Conversely, it's possible to write about supernatural forces without writing about religion -- because, again, "religion" means the cultural or individual practice of belief and devotion in those forces, rather than referring to the forces themselves. For instance, the recent
Avengers short films that aired online as prologues to the new animated series included a couple of segments revolving around Thor and the Norse gods defending Asgard from Loki and the Frost Giants. It was a story about divinities, but it wasn't about religion, because nobody in the story was shown worshipping the Norse gods or practicing rituals in their honor.