@layman,
1) he is gone The verb here is 'is'. 'Gone' is used here as an adjective. It's like saying 'he is tall' or 'he is finished'.
he has gone. 'has gone' is a verb form, the present perfect. The sentence means that sometime in the past, he went, so now he's not here.
So, technically 'he has gone' is correct: or you could try ' He has just left'. [Did you have had a bad relationship].
If it is in conversation and in context, then you would need the rest of the conversation to stop ambiguity.