As we've mentioned on occasion, God doesn't tend to turn up too often in Science Fiction, and when He does, it's as likely as not in the form of a slam on Him by some militant atheist. Christians, too, have their hangups in this regard. There's a tendency to make God play by our own sectarian rules in fiction. Either way, God tends to be used to illustrate preconceptions: If you're an atheist, then God will be used as a plot device to confirm things you already believed. Likewise, if you're a Christian, God is very likely going to be used as a plot device to confirm things *you* already believe. I'm uncomfortable with this preaching to the choir kind of stuff (On both sides) and I've generally advised that people who want to write religious SF should probably aim for the numinous aspects of divinity, the 'still, small voice' aspects of God, rather than attempting to make Him voice His support for the Missouri Synod Jehovah's Witnesses Separatist Revolutionary Church, or whatever. I think God is too important to be used for propaganda purposes.
Now, most religious SF (Pro and Con, Believer and Atheist) is drek. No getting around that, so I've always believed that the way to overcome the stigma that religiously-tinged SF has is to simply write a better story.
Lately I've begun to question that, however.
I agree that a part of "The Solution" is to write a good story, but I don't think that's all there is to it.
To a lot of people - Believers and Atheists alike - SF is seen as the purview of Secular Humanism, and no gods are allowed in the clubhouse. It's not just a question of a character's religious views being handled well or badly, it's that there's a considerably large segment that will not accept the character having religious views at all. There's a large number of diehard fans who'll go balistic at any mention of God or the supernatural or whatever becuase "There won't be any religion in space." I know a number of Trekies who won't watch Babylon 5 because recognizable human religions turn up in it again and again (Ivonova's an Orthodox Jew, Father Mallory is Catholic, I believe Lise is a Baptists, and I think we're supposed to believe that Catherine was Buddhist, though they never actually said. There are name-checks for the pope and the dali lama, etc) Some of these same Trekies are willing to tolerate Battlestar Galactica because it has hot naked chicks kissing, but that doesn't really help us out in terms of theological discourse, does it? And many still refuse to watch it because of the Cylon God, who turns out to be very much like the Judeo/Christian one, and not a delusion or alien or insane computer (Though probably Caprica will ultimately retcon that).
On the other side of the asile, in my church, there are people who don't believe any kind of religious SF can be done, even though it has been done many times, with varying degrees of success (Generally little, however: most religious SF is dredful). Opinion varies between "SF is evil" and "It is beneath the dignity of God to be discussed in SF." As a kid in 1979, I remember how upset people were that Satan turned up in the original Battlestar Galactica (And they made it quite clear it really was him) for just those reasons.
And don't even get me started on those folks who want to write "Lawful Science Fiction," ie cautionary tales about boring near-future dystopias decrying the UN, biomedical research, etc, and no one's allowed to write about aliens, the distant future, the distant past, space colonization, etc, because since that stuff isn't mentioned in the Bible, it's sinful.
I do totally agree that "Writing a good story" goes a long way towards fixing this, but the audience is pretty fragmented and ideologically driven. There's a lot of people on all sides who will find "A good story" to be a personal attack.