True villain speaks to the story as a whole, and not simply any steps taken by anyone which just so happen to have been negative/destructive.
So we would need motive and patterns to back up the idea that Hinata was the main hand behind the major villainy in the world of Naruto.
If we go with the "if", tho, then it would raise major questions about the actions of everyone in the story itself. How could the likes of Naruto (emotion sensing), Sasuke (perceptive) and many others (will of fire) not detect it? If somehow they did, then it leads to a conclusion wherein she changes nothing fundamental. If they didn't, then she is not worth bothering about in the first place because events still worked to a successful end.
In the latter case, her villainy proves itself meaningless. She would not be the 'true' villain but rather just a person who has a handle on high level events and is villainous, but only categorically.