To the people suggesting inconsistent characterization on Vergil's part I think that's a fair point. Allow me to propose a narrative to reconciles the ideas. Vergil was a child. No matter how realistic it would be, can you blame a child, who has just been stabbed, like a lot, begging their parent to make the problem go away? A child relies on a parent in a healthy relationship, and even if it's unrealistic, Vergil's emotional response would obviously be to want his protector, his benefactor, his parent, to make the stop the problem. But the deus ex machina isn't his family, it's himself. Even then, even after awaking something with the Yamato, his first action is to move toward his home. He sees it burning and knows his mother and brother are inside. What person assumes someone will survive a house burning down around them?
The next part is what I would consider my leap in logic. Imagine Vergil, by whatever means, finds out the brother he thought he couldn't protect, was still alive, but his mother was not. Dante, the brother he perceived as having been the one overly reliant on those familial bonds even before they family was destroyed, is still alive. Dante endures despite not understanding the inherent need for power as Vergil understands it. This makes Dante a living contradiction to Vergil's world view. "Mother abandoned me" or "you weren't strong enough" become less about being exact prescriptions of the complete situation, and more recurring tools to emotionally justify a worldview bolted into him by trauma. The funny thing about a tragedy like this is that it is basically random in the grand scheme of things. There isn't any deeper meaning into who survived and how between Dante and Vergil, just bad luck all around, coated in whatever emotional process they can use to process it.
Remember Nero's big point at the end of five, "can you idiots not kill each other?" Well, they could, but they'd need to come to terms with the fact that one destabilizes the other's coping. And to move beyond that is to understand that they still have family left, even if Vergil mades some very big mistakes on the way there.
I've been wrong before and I'm just throwing out ideas. Hopefully this does more good than harm. Or even makes any sense.