It makes me uncomfortable too, but it also isn't as though the show the endorsing it in any way. I think it's important to look at not only what is portrayed, but also how it's portrayed. The horror of this is exactly what you've said, that Amy has had no say and no knowledge of anything that is going on with her body, and we are meant to be horrified by it. I remember speaking with a much older professor once, about a story in which a woman wakes up pregnant and doesn't remember how it happened, about how this was the nightmare in the days before abortion was legal. It is meant to be a nightmare.

So yes, I do see where you're coming from, but the jury is still out on this, in my opinion. I don't expect Moffat to take it where Whedon would, which would like be an explicit (albeit perhaps ham-handed) commentary on the female body and its agency, but I also trust him to have given it some thought.