I haven't noticed any conflict between Evil key bindings and ediff. I can navigate between changes using j or k and select change with a or b. Can you give examples of what is in conflict? Are you using the now quite outdated version 0.200 of Spacemacs?

which window are you in when you navigate with jk? Let me try pulling the most recent spacemacs and see if that does the trick

The diff controls are in window 3, the small one at the bottom. I don't use ediff very often, but I have used it for at least a year without any problems. I am running Spacemacs 0.300