That John is telling Sam what Sam knows and believes about the REAL Dean: that Dean so loves Sam that he would kill Sam over allowing Sam to do something that would destroy Sam. And he is saying this is unique to Dean where he and Sam would choose differently, preserving Sam's life out of their own selfish need to keep Sam alive (something Sam also believes). Even while John is lying to himself (failing to know himself, IMO) and also, intentionally or unintentionally depending on your POV of the inside of John's head in that moment, lying to Sam (because if he told him the real truth, Sam would never believe it ... the truth to telling lies is to tell the ones that will believed as truth) inthat the parallel for this ultimate selfless act to prove how much better man Dean is than either John or Sam is, in truth, EXACTLY what John did in trading his life to the YED, but not his soul (which is how I will ALWAYS believe that trade should have played out and also a major reason I wrote this fic in the first place: to make that point with my reasoning for it), because he was willing to "kill" Dean (the damage he inflicts by knowing Dean will know John traded his life for Dean's) in order to save Dean from being DESTROYED, which is what John knows will happen to Dean if he ever has to kill Sam for any reason ... all of which circles back to John's point of proof for the REAL Dean over the YED Dean inthat the REAL Dean would have DESTROYED himself by killing Sam in order to save Sam from DESTROYING himself by killing Jo (ie; someone he loves, family, as Sam can survive killing an innocent even if the guilt plagues him for the rest of his life, but everything that is Sam would have been destroyed by killing someone he considered family ... also a point John fails to understand about Sam not shooting him in the Devil's Trap moment, as Dean would be saving Sam by shooting him -- an equitable trade in John's eyes --- but Sam would NOT have been saving Dean to shoot John, he would have only been destroying the demon, which was about saving HIMSELF from his future fate ... something that isn't important enough to Sam to sacrifice his father to it. The whole point of the story ... that both John and Sam fail to see their own depth of love as would fail to sacrifice their loved ones for their own salvation even as they recognize it in Dean, if not in one another.
So pulling this to a full (and I realize VERY confusing0 circle: that's why John can prove to Sam it wasn't the REAL Dean in Born Under a Bad Sign. Because the REAL Dean would have destroyed himself to save Sam from having to live with killing someone they consider family. So the Dean who DIDN'T make that sacrificial, self-destructive, choice? Can't possibly be the REAL Dean.
So in the long run, doesn't have anything to do with Jo VS someone they don't know other than in the difference the cost it exacts to kill family versus killing an innocent person you don't know. (not right or wrong, but cost to self ... think of how differently you'd feel if you had to choose between killing a stranger to save the world or killing your mother to save the world ...). Rather, it has everything to do with FAMILY and LOVE and SACRIFICE as all the Winchesters view them, even if John and Sam only really see that in Dean. Because Dean is Mary, while Sam is John. :D
Hope I haven't hopelessly confused you. I know this is an incredibly convoluted explanation, but hopefully it was cogent enough for you to follow my thinking to some degree. If you have questions and you want to risk another novel-length response, feel free to ask and I'll try to clarify if I can.