Cannot recruit Charon after defeating President Eden

[Shred]

I have just convinced the president to self-destruct and after leaving the base I have lost my previous companion, Sergeant RL-3.
Having an evil karma, I returned to the Museum of History expecting Charon to be available. I had earlier received his contract and he had killed Azrukhal.
This time, he is again standing in the corner ignoring me and Azrukhal is alive again. Sergeant RL-3 does not accept my recruitment order since I am too evil for it.