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.
Not wanting to get too involved into this discussion, but announcing the virtue of a religion to adapt... isn't that in essence saying, that the teachings of a religion are not set in stone?
And if that's the case, why have the religion at all?
If those teachings can be changed on a whim or be discarded just because there is new undeniable evidence to the contrary what is their actual worth?
What you are left with is the god of the gap to fill in the blanks that we have not yet discovered, and since we learn more every day, those gaps are getting smaller and smaller.
It will inevitably reach the point where god (any god) has to hide behind the threshold of unobservability, which is in what we call the big bang today.
But a god that can only exist behind that threshold has no influence on anything in the observable universe and can be treated as non existant and has no say in how we live our lives or how we treat others.