(Incidentally, I did wonder if maybe the librarian was a demon of some kind. Arkham used them, or created illusions or whatever with them, such as "Rabi". And the librarian was wriggling about in a way that the thugs weren't. A pretty creepy way, I might add. Didn't look quite 'human' when dying either... who knows).
I guess they had to provide some indication of proper motivation for Vergil in the manga, since the point was to expand a bit on the game story; but you're right, it makes things jar. If you think of them as both true, then Dante's attitude doesn't add up in the game, since Vergil has already told him about his diabolical plan to rule the world and Dante doesn't seem to pay it much mind in the game, naturally because the game happened first. It's a more casual first meeting in the game than in the manga I'd say, which is a bit 'darker', as a lot of manga adaptations seem to be... so the 'explanation' is suitably dark, too, I suppose. But it would explain why Dante says it's perfectly justified in killing Vergil to stop him getting Sparda's power... more so than just a suspicion that it would corrupt him, or that he couldn't handle it, or that Sparda hadn't wanted it to be passed on.