I don’t really see a lot of reason to doubt that he killed himself.
Regardless of how much we know about him from interviews or songs or anything he wrote, people still tend to keep a lot more than they let on under lock, even from close friends, so I doubt anyone that didn’t even know him personally could legitimately judge whether he killed himself or not simply based on how they think he felt about this or that and how they think he would have reacted to something.
Besides, I think people always want to pin the girlfriend/boyfriend of a rock star for something. People hated Yoko because she ‘broke up the Beatles’ – not John because he let her influence him, and totally forgetting that he was a Beatle, and would have just a bit more authority over the situation than a girlfriend – and people hate Courtney either because she made him kill himself, or because they think she killed him because she just ~couldn’t get over him~.