I feel like you're taking Yui's words/intention out of context a little. I've never been one to rush to her defense, but she didn't set up Instrumentality to say "Alright, enjoy your romping on post-3I Earth!" Her scenario was always about making the best out of the shittiest situation possible. She, mistakenly or correctly, assumed that 3I WOULD happen, so she put herself where she felt was best to derail it into a salvageable situation, if not stop it entirely.
Crazy? Yes. Malicious? Possibly not, I still can't think of a good reason to bring Shinji to watch her Contact Experiment that doesn't damn her at least a little. Sociopathic and nihilistic? Definitely not. She wanted to let humanity and her family pick their own destiny, not let SEELE dictate it. It was a REAL shitty road reaching that point, but it worked.
TL;DR: Monument to man stuck inside Unit-01 until it drifts into a star or something definitely means she's crazy, but she IS right: Humanity can make it out okay given the chance, and they got that chance.