Nora Allen is not evil. People trying to say that need to remember who Thawne is.
He's very manipulative and smart. He spent almost 20 years on just one plan before. Also Thawnes was the curator for the flash Museum in the future. Exactly where Nora spend most her time learning about the flash and her dad, since Iris refused to talk about her time on team flash and her life with Nora. On top of that learning she was lied too her whole life about her powers. ( not saying there wasn't a good reason). We already know that he lied to her since she was clearly shock to hear what he did in the past. He could have easily spent years gaining her trust, and using the broken relationship between her and Iris to his advantage. When he most likely told her about her powers, I'm sure he was more than willing to "teach" her about how she now had the power to bring her dad back.
Since Thawnes timeline is so confusing we don't know how they met, if he been in prison her whole life or if they knew each before. So we still have to wait and see what the whole story is. And if the make her just another villain who gains their trust and turns on them then that just poor and recycled writing from the first 2 seasons.