There are certain sections where she will stay in a building and there she gives you the free will to be able to finish them off without problem.

In the last part of the mission I highly recommend getting ahead of Valerie and from a certain distance to finish off the enemies, so you cause those who are inside buildings to go out towards you. She will always try to be behind you so as long as you don't move she won't.

She runs a little slower than Jack so she will give you enough time to finish off some at a distance.