The joke mention God and abortion in the same sentence, and in a thread about wacky Christians. If you don't see the implicated tie-in the baby abortion, you're even dumber than your screen name.
God decided he wasn't ready for the Rapture, so he had it aborted.
Here's the key. What you wrote, Rhett.
Also, look at the specific wording.
"... so he had it aborted." That's the type of phrasing that is usually used for aborting a baby. If it were a rocket launch, it would usually be "... so it was aborted." Nit picky, I know, but that's the subtle communication within the art of the joke, if that's what you could call it. Besides, Doom has on occasion made several references in the past about never wanting kids and other eugenics sort of cracks towards various groups of people. There's a pattern there.
As I said before, I am pro-choice but I will call a spade a spade when I see it as such.