I don't agree that it was for shock value. The demon spawn is an heir to Mundus, and would at some point become just as much of a threat to the world as Mundus is. Similar to the "who will take Mundus' place when he's removed from power," Vergil was removing a threat from the equation, along with Lilith, who could just try to make another one. Knowing this, how are you to go about doing something like that? Would you have rather had Vergil take Lilith to an abortion clinic and get it done all official-like? And
then shoot her in the head...? DmC is still a Mature-rated game about demons and killing, and even the old series wasn't above people being chopped up, shot, and straight up impaled - sometimes for dramatic effect. Why did Alastor need to impale Dante? Couldn't they have written it so the sword didn't need to do that? Couldn't they have written Dante killing Sanctus differently, instead of him flying in and shooting a very human-looking pope? Yes, they could have written things differently, but they didn't want to, because they had a specific idea in mind. Why is DmC not allowed to have something similar related to its story happen, that fits with the more mature tone in place?
Plus, Dante and Vergil being Nephilim, they can surely handle a human SWAT team with ease (spoilerstheytotallydid).
I don't suspect Vergil knew that Mundus would level a city block in anger, but hey, when you're blinded by your own selfish goals, you tend not to think of the consequences beyond your reasons for doing what you did. Granted, I wouldn't think a guy who runs the world through deceit and subtlety would do something as conspicuous as level a city block