[So Jon was going to hang himself, then Ben stops him. But Jon tells him he's with that one guy then Ben strangles him to death. Then Jon is reincarted (someonewhere) on the island, and Ben there with them? ]
Yes - although most people were under the impression that he committed suicide (due to all of the preparations John had made to do so), he was actually murdered. Why he was murdered still remains a partial mystery...I think that Ben already knew who John was working for, but wanted to find out everything that John knew about who to talk to/what to do so that he could return everyone to the island on his own terms.
John was revived/reincarnated upon his return to the island (he was in the coffin in the cargo hold), leading me to believe that the "you're gonna have to die, John" line was only technically true. Either way, I'm glad that Locke is back