Okay so maybe this theory has been floated before, but despite the end of the latest update, I really don't think this game is going the incest route with John and Mia. Mainly cause I really don't think she's his actual sister.
What I mean is, she's probably the sister of one of the guys who were killed when he was taken captive in the flashback. From what little I know regarding people in the army, which mostly comes from books and movies, lol, but they tend to form pretty close bonds, and he might have considered them as close to being family as someone could be.
So when he finally got free, and eventually ended up going home, he probably took on the role of being Mia's brother since her actual one had been killed, and he wanted to honor his memory by protecting the sister he probably cared about alot how he thinks the guy would have wanted.
Heck, he probably knows full well Mia has a crush on him but ignores it because he's supposed to be her brother.
That's just my guess though. Seems more likely then a girl admitting to a total stranger that she has the hots for her brother. lol