Your post made me think of something. I know I am going to regret for writing this; but what if Historia is not miserable, because of the pregnacy but because she absolutely hates the farmer?

In 107, we can see Historia looking at the sunset while touching her belly. Her face is not shown. The same goes for the next panel. However, here the farmer appears and talks. In the next panel, we finally see her face; she looks annoyed as if she says "You again?". When he stands in front of her, she looks at him angrily. Her hands are over her belly protectively. She'd have been relaxed if it were someone she trusts and cares about, someone who was not be dangerous for her and the kid right? But, she did not.

I do not know if he is the father of not, but to me it seems that she hates him. It'd would not surprise me if he it turns out that he's working secretly for Zeke and Yelena.