Yep, it's more of a sense of 'how can you be stupid enough to even think of attacking me.' Mundus has too much pride in himself and his powers to even think someone would stand up to him.Ithink that in this case Mundus is surprised not because he thinks he is in the right, but because he thinks he is simply too powerful for anyone to attack him. Vergil, on the other hand, is surprised that Dante opposes him because he thinks to be in the right.
As for the sequel, that would be interesting to see, but I think that after VD now Vergil is set on demonstrating that he is more powerful than Dante, he is no more interested in having him as an ally, now he just sees Dante as a rival to be surpassed (just like he is doing with Hollow Dante).
You're right. This new Vergil would be more likely to want to kill Dante, just like in downfall to prove that he is the son of Sparda. Vergil wouldn't want anyone getting in the way of his plans, especially his brother.