The only ways in ETM I know of to kill Agents (Smith included) is to hit them with 3 grenade blasts (either hand grenade or grenade launcher) or to use the gas gun which I can't recall the name of.....you know, the one you get on the reactor stage.
Since none of those three items are available on Vertigo.......I have no clue. I know you get grenades on the China Town levels with all of the Smith's chasing you (out of police car's trunk).......but as for the Skyscraper level (vertigo) I have no clue.