My stepdaughter DID have cancer (leukemia), and whether or not she was gay or a believer was the last thing on our minds. My wife was a Mormon at the time, and I can tell you, children at that age are not allowed to choose their religion. So whether they are atheist or not is moot--they never get that choice.
I was an "agnostic" at the time, when my wife and I started seeing each other, and I was not anti-religion at all, and was quite fine with her being a Mormon. The church gave us a bunch of trouble though and excommunicated her, although they tried to get us to let them take the kids for indoctrination.
We didn't let them, but later as they matured into their teens, we never stopped them if they wanted to go to any church. The child with Leukemia was successfully treated and went into remission and her cancer never came back. She later befriended a group of nondenominational Christians when she was in high school and I didn't stop her--in fact, I drove her to church. As she continued growing up and finding other friends, she stopped and now leads a mostly secular life. Not sure if she believes in a god or not--and it's not important to me, because although they were indoctrinated as children, my wife and I actually gave the kids a choice and stopped letting other adults force them to go to churches, Bible studies, etc.
If I had a gay child, I would accept and love them the same. If they chose religion of their own free will, that's their choice--and I wouldn't be happy about it, but I certainly would not treat them bad as long as they didn't try to push it on me or other family members.
Hope this helps.