I think you sort of missed my point. When the series started, I liked JJ. The early version of her character was well written and for such a dark show, her sweetness and light balanced out some of the gross characters we had. She was written to be human, but also someone who treated others with respect and kindness. The first time we really saw her as, lack of a better word, a selfish bitch, was 3x17. Will was someone who was supposed to be important to her, someone she had been dating for over a year but she treated him horribly. She was snotty, mean and condecending to someone who seemed totally devoted to her happiness. Will wanted to be acknowledged as a part of her life but she wanted things her way, end of discussion. It was her way or the highway which is a pretty hurtful way to treat someone you have been in an exclusive relationship for over a year. Will and JJ's whole relationship is written to be all about JJ. She has to always be right and always get her way and compromise doesn't seem to be a part of her vocabulary anymore. Relationships are supposed to be about give and take but as it's written, JJ takes and Will gives and gives and gives.
Way before they fired AJ, JJ was starting to change and not for the better. Sure, the change was amplified after she came back but it was there already.