‘He is gone’ denotes a state and not an activity. It refers to the absence of something or somebody. By the time I came down, she was gone. When we want to convey that something or somebody has disappeared or is no longer there, we use ‘is gone’. My book is gone. My watch is gone. Is the coffee all gone? They were all gone when I came back. ‘
He has gone’ means that he has moved out in some direction or to some destination. You are aware of some of the activities relating to his going. You can say: He has gone out of the room. He has gone home. They have gone to the temple. You can’t say ‘He is gone to the temple’.