Glargg, I usually really like your comments, but I have to disagree with you here.
She was never on "our side." She is a servant of Molag Bal, who gave not only herself but also her daughter to Molag Bal to become daughters of Coldhabour. She is a necromancer who opened a portal to the Soul Cairn to become a more powerful necromancer. It backfired on her, but her intent was hardly a good one.
She opposes Harkon, not because she does not work for the Vampire kind, but because she thinks Harkon's plan would backfire on vampires and wind up getting them eliminated. So she shut her own daughter in a crypt for several centuries with the scroll. This same daughter that she told you was expected to give herself to Molag Bal to be violated, cause that is what her family was into. Serana herself says in the Soul Cairn that she now realizes that her mother was no better than her father, they both just used her as a pawn in their own power scheme.
And the Dawnguard are vampire hunters. Valerica as a Vampire Lord is one of the worst of her kind, and is still a daughter of Coldharbour, so she could still be used to make the prophecy about eternal night come true. I don't recall that Harkon was the only one who could make that happen -- rather, he was just the one who wanted to make it happen.
So from many angles, leaving Valerica 'alive' at the end of this storyline seems to me to be a mistake. I can see that Serana may be an exception, and if played right Serana can be converted to cure her vampirism. But Valerica, not so much. Seems to me that a real Dawnguard type, a vampire hunter, would go back to the Soul Cairn once Harkon was ended (or even before that), and make sure that Valerica was also terminated.
But still, no one has answered my original question: does anybody know a way to do it? Is there any way to kill Valerica?