I feel like Yuko just went off, telling Gen how to trigger Reiji to get him to kill him.
While he has some feelings for Reiji, he also has them for Yuko so I don't think he ever would kill her.
Also Gen's just really confused about his feelings and where he belongs. Maybe he IS Gay but to me it looks more like he just wants to be happy with a mother and a good friend and that's why he said he loves them. He feels dirty because of the murder he did so he wants to revert back to be a child or dresses as Yuko who he looks as pure. Maybe I'm wrong but right now, that's how I read the situation.