Ok. So. Now we know the context of why Itto pitied Kondo for being surrounded by fucking nutjobs. He didn't seem to dislike Kondo, in Guda Guda timeline.
Turns out Okita and (specially) Hikijata were absolute Kondofags, in that they wanted to make Kondo the shogun, with their nutjob clique. Kondo's ideals were never about that, but he passively went along because they were intense and felt he couldn't stop him, but rather meet their expectations as their leader.
Instead of being captured, in Fate, Kondo surrendered himself to stop the shinsengumi from murdering each other, hoping that would set back things peacefully. He asked to be executed in exchange of a pardon for everyone else. Like history, Hijikata got to beg Katsu for a message to save Kondo and got his support, but Kondo agreed to die for the sake of peace and his subordinates to be spared. He made himself the scapegoat of all their decisions.
After death, he found out shinsengumi got glamorized and couldn't accept it until the Nobbu made him regain faith in himself and heal him to be able to proudly raise the flag of truth (true) this time as he dreamed before all went down to the hell.