Someone asked recently why I couldn’t write “nice Christian stories”. Answer: because I can’t.
There’s a tendency of modern western evangelicals to cloister, or enclave. Christians only associate with other Christians, go the Christian Schools (or home school) work for Christian companies, live in Christian communities, shop at Christian stores, read Christian books, listen to Christian radio, watch Christian TV… It’s safe, it’s predictable, controllable to some extent, and it’s a fantasy. The salt stays in the saltshaker and the light is safe under its bushel basket.
Life isn’t Disneyland. For most of the world, life isn’t even America, and for much of America, life isn’t suburbia. This is my Father’s world but it is not Christian. The real world is a messy, dangerous, beautiful place. Now I believe God has a passionate concern for His creation and the Gospel is the mind-blowing news that He offers genuine forgiveness to real people who have committed real sins in our real world. The struggle is to accept that with all it’s brutal ugliness and awesome wonder, and effectively pass it on.
“Running Black” is fiction, but I made an effort to include Christian characters in an organic way in realistic settings. I wanted to avoid creating a “scary but safe” adventure, as if it were some sort of theme-park ride where you’re titillated but not touched as you wind towards the happy ending. I wanted more “gritty realism” than goose bumps. I included a bit, a tiny bit, of abrasion and discomfort; not gratuitously, but because I felt (believe it or not) a conviction to do so. This conviction of realism factored in everything from my decision to avoid light sabers, aliens, FTL space-travel, to name real cities and companies, as well as to let my non-Christian characters say and do non-Christian things. Explicitly. But I wanted the Christianity to be just as explicit.
Did I execute that conviction in my first novel perfectly? No. But my inability to do it perfect wasn’t an excuse to leave the task undone. I’ve got more stories inside and I pray to get better as I continue.
Hot Space Station Justice 
Religion and science have long been (wrongly) considered opponents in the struggle for the hearts and minds of humanity, and science fiction readers have historically come down overwhelmingly on the side of science. In light of this, any religion at all in science fiction is an inherently risky move.
That said, I think you took a fairly conservative (from the science fiction side of things) approach in that while you have Christian characters, they are sensible adults as well. They do what they do and live with the risks they take because they believe it’s the right thing to do. There’s remarkably little contrast between them and the mercenaries who do what they do and live with the risks they incur because it pays very well.
The antagonists in the story (if memory serves) are in some cases also religious and sensible. It complicates matters for any sensible human being when the people on both ends of the gun barrel pray to the same God.
This is how the real world is: complex, messy, and often morally ambiguous. It’s not for weak minds who want scary-but-safe.
-JRS