Sure. All the characters are doing their best, even when their best is actually not that great — that’s good writing.
But Nodoka’s “higher purpose” is no excuse for being needlessly cruel. At least with Yumi I can see what she’s reacting to. Kirin is just a walking ball of libido, and does some things that are beyond not okay — but she doesn’t do them just because she can. She does them because she desperately wants to get laid. Ami is batshit — and I think Sensei is only partially responsible. Io isn’t great with people (other than Uta and Sensei, for some reason). All the other characters do things that hurt others. But they do so while trying to achieve goals that we can understand. Sort of. (Love ya, Yasu!)
Nodoka, though? I get her dedication to her “art,” I really do, and the in-game logic of her trying to do… whatever the fuck it is she’s trying to do.
But as you say, it doesn’t make any of it acceptable.
If it turns out she’s a direct conduit to one of the “gods” like Yasu, Kaori, and Tsuneyo seem to be, I’ll at least feel as if there’s some excuse. But acceptable? Nope.