"In the early script drafts, John was a secondary character. Producer James Middleton explained "Ben-Hur was influenced by Jesus Christ, but it was his story. Much in that way, this [new main] character will be influenced by John Connor."[54] The original ending was to have John killed, and his image kept alive by the resistance by grafting his skin onto Marcus' cybernetic body.[55][56] However, after the ending was leaked on the Internet, Warner Bros. decided to completely change the entire third act of the film.[57] McG and Nolan did continue the Christ element of John's character though, in which he has some followers who believe what he knows about Skynet, and others who do not.[58]"
McG said in interviews there was another ending where Marcus-as-John shot everyone and Skynet won, so it sounds like it could have gone either way. However the key point was Marcus replaces Connor in the timeline.