Maybe she can be pregnant after this, but considering she wouldn't know until after a month maybe it is season 2's cliffhanger. It could be a nice turn to the story, maybe she could pass it off as Burke's.
When one like is not enough, but you don't want to click the like button twice like a retard trialpha.
EDIT: I'll expand a bI it more. I think you are completely right. And I don't say this lighly. There are major flaws in that scene.
The DIK system, for one. I think it's a good system when you can tell what's going on. When it blocks (and tell you why) it blocks certain actions, like the DIK helmet and tells you why, or when it makes the MC say different things. When it changes the line you say to compliment Jill from "You're so hot, gurl" to "Wow, that outfit looks nice on you". Then you can tell it's working. But in that scene we weren't informed it was blocking something from us, or we weren't forced to choose something because alignment. It just happens because reasons.