I’ve never actually talked about Naminé’s feelings towards DiZ/Ansem the Wise, so let me just. Give that some perspective because I am a salty bitch:
When DiZ first approached her, she was grateful to have a second chance for redemption. He was that saving grace to get her out of that godawful castle and see what was outside of it.
But she very, very quickly became aware of what she was to him. A means to an end. The longer she spent around him, the more she realized how much of a bitter man he was. She couldn’t tell if he was better or worse in than those who resided at Castle Oblivion at times.
Naminé then became more self aware, wanting to go beyond just helping chain back together Sora’s memories. She grew defiance (I’m fairly sure Riku was apart of her growing a rebellious side).
She knew that DiZ would eventually want to get rid of her, so shortly after everything that happened with Xion, she asked Riku to show her how to work the computers since he was around DiZ the most during that year.
It was when Riku brought Roxas back wearing his hood did she start to outwardly question DiZ about his motivations. She knew what happened was wrong, she was absolutely furious that DiZ pushed Riku to do whatever it takes to bring Roxas to him. She was even more furious that Roxas was brought back in such a state.
It’s after Roxas is put into the Twilight Town simulation when Naminé gets to work on hacking the system and inserting herself into Virtual Twilight Town.
Through all of the verbal abuse DiZ sent her way, it fueled her rebellion more to want to put a pin in his plans. She knew what it meant, but no longer would she be a pawn in somebody else’s plans to hurt the people she had grown to care about.
She begins to openly question him about why he’s doing any of this and how any of it makes sense. Any time he tells her to do something, she immediately shoots back with a question.
Her magnum opus for her rebellion was downloading herself into the virtual world in order to properly help Roxas understand who he was.
Also at the end of the third game, she absolutely gives him the cold shoulder. Not even responding to any of his questions, she only really responds to Ienzo and maybe Even.