How can you separate John's "apology" from the duress and fear he's experienced and which, he says, continues to plague him?  He's a fugitive -- or at least he thinks he is.  He describes break-ins and harrassment directed against him and his family that have scared the hell out of him.  He's been ostracised by all his old friends (Well, what do you expect when you're dissing their cult leader?). By his own account he's suffered a breakdown and considered suicide.  He's in therapy.  He doesn't know where his next paycheck's coming from and he's obviously scared shitless of Maharaji. In short, he's got a gun to his head.

How can you not take his apology with a grain of salt?

You know what you sound like?  You sound like some Islamic terrorist who's got some hostage "apologizing" for the sins of America on tape.