I don't think that "If you were here" in this context can legitimately refer to a hypothetical situation in the past. In casual speech, maybe, but not if you carefully analyze what's going on with the tenses.The difference is the following:
1. "If you were here, I would have killed you with my bare hands. = 'were' is used to express unreality in the past, i.e. you were not here (sometime in the past) and I didn't kill you. The whole thing is over now.
2. If you were here, I would kill you" = 'were' (past of unreality) is used to express unreality in the present, i.e. you are not here now and thus I haven't killed you. But you never know what can happen (in the future) if you show up any time later beacause I'm still very angry .
N.B. Another possibility to express the same as in 1 is : "If you had been here, I would've killed you with my bare hands."