When was the last time you made a woman cry? He clearly told Historia his plans and that's why she cried, since before she had a knack for getting words out of Eren, it stands to reason he told her his plan, and if he did it means he did it before telling his sibling and his childhood friend, which means a lot.
The story also focuses on the themes of pro-natalism vs anti-natalism.
Any way, if I wasn't so lazy I would go count the amount of non repeated words (like ereh) Mikasa has said to Eren compared to Historia with time taken into account but oh well.
There is obviously the chance he isn't the father obviously since Isayama likes to break muh expectations but, if he does it like people suggest with having her have a child with the farmer then Isayama truly would be a hack.