Until "Forging Bonds," yeah, I assumed that Alex was referring to some sort of romantic betrayal. I absolutely can't see Neal ever cheating on a romantic partner. Loyalty is too important to him. But I wondered if he hadn't been falling in love with Kate and refusing to admit it to himself until Alex finally had enough. But then I saw "Forging Bonds" and that was quite clearly not the case. It was less a headcanon than a guess, and I wasn't sad to be wrong. (Because, yeah, women's storylines revolving entirely around boys.) But I was always frustrated to never learn what actually did happen.

I am completely for anything that makes "what happened with Kate" actually about Kate and Alex. Alex's complete lack of reaction to Kate's death has always deeply annoyed me.