I thought she said he wouldn't take a position and that's what fucked Zion upMorpheus and Zion are way too large of a plotline for them to just write them off like that and imply some shit.
They coulda cut that 20 minute bullshit montage of them workshopping how to reboot the matrix and actually explained what happened
We dont even know where Morpheus stood when it came to working with the machines or not