The movie was Unforgiven, and I think you have your scenes mixed up. At one point the kid refers to man he just killed and says "he had it coming" to which Clint replies, "We've all got it coming, kid". In another scene Gene Hackman has just been shot by Clint and is dying. He looks at Clint and says "I'm building a house, I don't deserve to die like this", Clint replies, "Deserve's got nothing to do with it."
He had it comin’ can mean he deserves it. But we do all die, so the last remark puts a more fatalistic spin on it. Have you forgotten the critics judgements that the pciture had an almost religious tone? Eastwood himself was puzzled, as he probably does not have a relgious bone in his body.