Well, I also assume that finding alien life will cause some major religious upheaval as well, changing a lot of belief systems drastically. But I would consider a nuclear physicist a high science position that a creationist could fill without much problem, so why not a ship's engineer? It's admittedly quite unlikely, but it's not outside the realm of possibility. There is a certain level of suspension of knowledge to believe creationism that I don't fully understand, admittedly, but I don't think it would eliminate them from EVERY Starfleet position.
I also don't see all religions disappearing overnight either. In fact, if there was a WW3, they would strengthen before they weakened. And most modern religions have been around a long while - like over a millennium - I don't see them just up and fading away into nothing in the next 2-300 years. Even if there was less fundamentalism than there is now, there is a basic human need in a lot of people to believe in some sort of afterlife/deity/whatever.
Somehow I think our religions would adapt quite easily. They've shown extreme elasticity. So much so, the first warp-capable ship heading to the alien world would have missinaries to show the aliens the light.