Not really sure what in the second book made you think she was meant to be a villain. The end of her plot in that book is murdering the shit out of slavers.

It's made obvious that her idealised version of what will happen when she tries to take the thrown won't pan out and she's ignorant of how awful her family history really was, but I don't think she's intended to be a villain, just a complicated protagonist who, like the rest of the cast, is going to have a low point where they probably end up doing some awful shit before redeeming themselves fighting to save the world.

The leading consensus on the aSoIaF people I still follow is that basically that the TV show probably swapped the order of events for Dany's low point and ending. So she does the save the world thing, then the awful thing, completely changing the context of it and just suddenly making her the main villain at the last minute out of nowhere.