SG-1 isn't atheist. It's Gnostic. Gnosticism is one of the earliest Christian heresies (directly addressed in the New Testament, which was written in just the few decades after Christ, so very early) that was built on the idea that matter is bad, we're imprisoned in it by the false God (the God of the Bible in real Gnosticism), and that by the possession of the secret knowledge of gnosticism, you can transcend your earthly existence to become pure spirit, which is good. Anything keeping you from that is evil. Gnosticism also perfectly well fits with the material world being quite evil, and all the "false gods" running around fits in with that.
The Gnostically-transcendant "Ascended" beings also decided to not interfere with the material world, except for a couple of rebels. Those rebels were also portrayed as basically being wrong; both rebels in SG-1 also made enormous mistakes and the universe would have been better off if they also stayed hands off, and the Ascended were correct they shouldn't have done anything. (I would consider Atlantis more ambiguous on this point.)
When I say it "is" Gnostic, I don't mean that they were pushing Gnosticism per se. I just mean, that's the fundamental setup of the universe. The Highest Reality shown is Ascension. It would be a rational conclusion in that universe (though not the only rational conclusion, but a rational conclusion) to conclude that the only goal worth pursuing is Ascension. (In fact it was a bit jarring to me in some ways that the characters did not address that more fully at times.)
The show's Gnosticism doesn't seem to have included the particular idea that we were imprisoned in the material world on purpose, but it has pretty much everything else about it.
So bear in mind I mean this descriptively, not proscriptively; goodness knows I'm not advocating for this myself. I'm just saying that just as the Lord of the Rings is established on certain ultimate principles spelled out in the first section of the Silmarillion, the SG-1 universe is at its core, very Gnostic. I don't mean this as a good or a bad thing, just a descriptive one.
In fact a Gnostic would consider responding to the universe with atheism as a reasonable one to some extent, because the material world has nothing worthy of worship in it. They would just claim that there is still something better, to transcend the material world into pure spirit, but if you didn't know about that, atheism would be the next reasonable response.
(The ideas of Gnosticism can be further traced back in the mythologies of the area, like Greek and Roman. If you get early enough versions of the myths and read them with the mindset of the time, or read the philosophers of time, most of them also had some variant of the belief that life involved eventually moving into the pure spirit world, sometimes in good ways, sometimes in bad. Given the nature of the show and its relationship with mythology you could come at it that way as well. But it ultimately still strikes me as fairly Gnostic, rather than the older mythological interpretations. YMMV; if you know enough about this sort of thing to have opinions you are welcome to them by me.)