I actually don't understand where the feelings came from at the end of the series. Sekai was completely willing to, and even forcing Makoto to try harder with Katsura. Even if she did like him and was using it to have her way with Makoto, she was still more concerned about Katsura's feelings more than her own. Once Makoto starts sleeping with all those other women she begins to seem distraught, but not entirely too much. She ends up making up the story about the baby in order to have him all to herself. When He decides to ditch Sekai and go after all these other women (eventually ending on Katsura) she tries her best to get him back.
So where did these murderous feelings come from? She was willing to share, even push Makoto away in the beginning. Though she seems troubled and even tries to make up a story about being pregnant I see no reason why those feelings would have lead to murder. If she had actually been pregnant and Makoto was ditching her AND a baby then I could totally see the killing intent. I'm reminded of one of the saw movies where
The guy saws off his leg in order to save the wife that he was cheating on. You obviously didn't love her enough not to cheat on her or to stay with your daughter so what the heck is your motivation so saw off your own leg for them?