To be fair, she's kind of evil herself. Side with the Dawnguard? She'll help you storm Castle Volkihar and destroy the vampires, as long as you kill her father. Side with the vampires? She'll help you storm Fort Dawnguard and destroy the humans, as long as you help her kill her father. Don't let her fool you, as she said, she's "nothing if not persuasive". She isn't as sweet as she'd have you believe, she's using you for her own patricidal ends, and she doesn't care who gets killed along the way.
Well, to be fair; it's not like the Dawnguard are entirely squeaky clean given the fact that Isran seems to believe that ALL vamps are inherently evil. Skyrim's recurring theme seems to be making both sides of a conflict morally grey. Besides, Serana only sides with the Dawnguard if you're in it since she knows you're the only one to not stake her on sight. Plus, most of Castle Volkihar's vamps (besides Harkon) seem pretty chill with where they are. Yes, the have abducted people to feed off of, but they aren't actively trying to blot out the sun like Harkon is.