I also think so, that JJ stays with Will because of their son
Remember in "JJ" she told Strauss that working at the BAU makes her a "better mother" not a better
wife/fiancee and at the end of the episode she calls the team her "family". Never in this episode was Will ever considered as part of her existence so it seems so random that he'll be back now
And Hotch does totally seem hurt when he says "We will leave you some privacy" then "You could have told me". It's like he wished he could go back in time and take better care of her
I hope TPTB won't ruin everything but as you just said it seems very clear to me that JJ's heart belongs to Hotch and the other way around as well
