All we know about John we get from Dean and Sam and neither one of them is a reliable source of info when it comes to John.
I also believe that while he might have told Dean that they might have to kill Sam one day, he would never have done it. He might have believed that in order to save his kid he would, but I just can't see it. He might have seen the world in terms of black or white but it's a whole 'nother thing when your kids are involved. Parents will do almost anything before they'll admit their kids are a write-off. I doubt he could have, any more than Dean could have. That's my opinion.
I enjoy a horrible John occasionally, if it's well written it can really drive a story. But making him the MOTW just because you can't create your own characters or monsters...*shakes head* I'm judging.
Mind you, I haven't forgotten the story I wrote where John was a murderous, drink-addled, child abusing monster.