Your hypothetical “if Reuven intended to kill Johnny because he hated Johnny, and it just so happens that Reuven killed Johnny while Johnny was trying to kill someone else, saving the life of an innocent victim, did Reuven commit murder if he had no idea that was happening and that was not his motivation?” does not seem very related to your OP, in which it’s hard to argue that he had no idea that this was a dangerous person.
Are you asking a general question about a muttar act where the one committing thought it was assur? Or are you asking whether hatred of a murderer is actually good as a manifestation of love for the victim, in this case, ahavas Yisroel?