This bit was patched together from a few different stories that were told to me over the years from friends and strangers. No one ever told me personally they wanted me to be the father of Jesus' baby, but trust me, it's happened.
I think part of it is that a person who is convinced that they have to have unprotected sex with random hitchikers by divine mandate is probably also less likely to worry about things like STDs or safety. It could also be possible that she'd do something to the lads afterwards so that her kid would grow up fatherless messiah or some other fantasy. Not to mention I don't think Peter's really in a place in his life where he wants a kid, nor is he the type to abandon one like she wants. In addition, if it was just about sex for him he probably would've stayed with Kara.
If I had the same choice I think that I too would have chosen the spookshack.