If he felt that way about her, then why did he decide to lay up with a woman and bear a child? It's obvious that he cared for her, and blames himself for not being strong to save her. Like how Vergil lost his mother when he was young that emotionally scarred him. And he even said to Dante, "Might controls everything. And without strength you cannot protect anything." That meant that he cared about someone he loved, but he failed to protect her. So it drove him to the path of the dark side and forsake his humanity. Because, he sees his human side as weak, inferior, and pathetic.I'd personall try to veer away from the whole "Virgil falling love" with a human woman. I like the idea better that Virgil simply laid with a human woman in a vague attempt to understand and emulate his father Sparda. In his desparate attempt to comprehend why his father would take interest in a being so beneath him he completely misses the point of why what Sparda and Eva shared was so special. Virgil believing that his efforts were a fruitless attempt, feelings he's wasted his time leaves. Unknowingly Virgil concieves Nero who later finds out that he's nowhere near as strong as he was his age consider him a weakling.
So it would make sense that losing a person he loved took him to a dark path. (Similar to Anakin Skywalker turned to the dark side and became Darth Vader. Where he lost Padame out of his own anger that caused complications of giving birth to twins. And he hated himself so much that if anyone mentioned the name Skywalker, will be brutally murdered by Vader.)