It also doesn't bother me as much (with no dictation to other people's feelings, just noting) because it's actually her pregnancy and while its circumstances get all weird and fucked up, it obviously started because she and Rory were at least open to the possibility (I mean, lord, they've been sexually active together HOW LONG and not had a pregnancy issue before now? I think they know about birth control).

Eye-patch lady then brought the Creep, but it wasn't something Aliens Did To Amy fundamentally. TARDIS-weirdness altered the baby, and enemies then pulled screwed up shit during the pregnancy, but it didn't start there. It started with her and Rory and an obvious choice at least to skip the condom/pills this time.