Firstly, yes, a lot of people do put their own feelings into this character and it's why we have several people who keep thinking there should be a "3rd option" to cut them off completely because that's what
they want to do, but it's not what the MC wants to do. This has certainly contributed to a lot of the ill feelling towards M&J because rather than put themselves in the MC's shoes, people are putting their own shoes on the MC.
Also, as far as the in-game story timeframe is conecerned, I would also add that whilst it is 2 weeks for the MC, it's a lot longer for players because of the wait between updates, and that allows people to think a lot more about these characters and really get attached to them, so that likely also contributed to M&J hate as feelings will have deepened the more people thought about them making the ep 4 events hurt more.
However, I would disagree with a couple of points.