Yes, she is a protagonist of the story, that in no way means she as a character can't be considered a villain. She absolutely has slaves, or at the very least had them even if she doesn't currently.
Landa and Silva were villains of The Basterd's and James Bond's stories, but imagine if the stories were told from their point of view -the Basterds and Bond suddenly become the villains. No one thinks of themselves as the bad guy. Silva consider M the villain and himself the hero. With characters like Dany it's all about perspective. Dany has and intends on doing some pretty stuff, she's not the audiences villain, but she's definitely someone's.