It's more of a case of unreliable narration and elena not understanding the prince's situation, in some spoilers i read, in the OG timeline the prince came back looking for elena, but veronica had already taken her place, he knew immediately she wasn't elena and killed her, then went looking for elena but by the time he got there it was too late and she was already dead, the last we see of it is him apologizing in tears to her for not being there to save her, and yes he did deeply love her, and yes he's the ML