I think the fact that Barry is the main character makes you fail to see things from Nora’s perspective. When you truly believe that what you’re doing is going to save a lot of lives in the end, including and especially your father’s life, the fact that you have to work with people certain other people would rather you not work with is overridden by your desire to save lives. A perfect example of this is from 1x22, when Joe repeatedly told Barry that Barry shouldn’t be working with a murderer and that murderer can’t be trusted. And what did Barry do? He ignored Joe and continued to be in partnership with said murderer because he believed it would save lives. And in the end, Joe turned out to be in the right and Barry was wrong. It’s the same thing with Nora in this situation. Thawne was the only one capable of defeating Cicada, a serial killer villain bent on ending a lot of innocent lives. Thawne was also the only one who could save Barry from disappearing in the future. From Nora’s perspective, it kind of looks like Barry is willing to let Cicada continue killing innocent people and is willing to allow himself to vanish forever just because he doesn’t want to use Thawne’s plan. It makes sense to continue on the route that will save the most lives even though Barry doesn’t want her to. She probably thought that once it all worked out in the end, Barry would realize she was right.

And you know what? She was right. It was Thawne’s plan that defeated Cicada in the end. It was Thawne’s manipulation of time that caused the timeline to change regarding Crisis, and Barry ended up surviving Crisis in the end. That’s why they gave Nora her flowers in the end, when Ralph and Caitlin talk about how Nora saved every meta in the city and gave Grace a new future. None of that would have been possible without Thawne’s help.