Explanation: John lives
This is a slightly altered reality. I didn't want John to die and so, in my world, he didn't. This is how 'In My Time of Dying' went in my world:
Dean is fighting for his life, running from a Reaper. Sam is trying to find a way to save him, but is coming up empty. John, knowing that they are running out of time, does the only thing he can think of. Since the only true way to call off a Reaper is to bind it and switch one life for another, John has to be creative. He calls up his sworn enemy and makes a deal - the Demon gets the Reaper to back off so that Dean has a chance in exchange for the Colt, the only weapon known to defeat it.
The Demon agrees but has a few tricks of its own. First, rather than talk or try and bargain with the Reaper, the Demon simply possesses it and wakes Dean. This fulfills its part of the deal but it also knows that Dean has now escaped two reapers and that they will certainly be on the look-out for him. Also, by pulling Dean so abruptly from his coma, the Demon knows that there is a good chance that he will have lasting medical complications if he is even able to leave the hospital (alive and on his own).
The second trick the Demon has up its sleeve comes to a head when he visits John to collect the Colt. Rather than taking the gun and disappearing, the Demon sticks around to give John a taste of what Dean suffered at the cabin - only, instead of trying to bleed him dry, the Demon squeezes John's heart to cause a heart attack. Once John has stopped breathing, the Demon leaves.
However, Sam walks by his father's room and sees him lying on the floor and calls for help. The doctors are able to resuscitate John. When John wakes up and is told what has happened to him and to Dean, he figures out what the Demon has done. He realizes that it is still too dangerous for him to be with his boys, citing the events at the cabin as his main argument.
John and his boys go their separate ways once more. Over the next few weeks/hunts, it becomes obvious to Sam that Dean is upset about what happened. He discovers that Dean feels responsible for John's disappearing act, not to mention the loss of the Colt and John's heart attack. He blames himself for cheating his father and brother out of the only weapon they could find that would destroy their enemy and get the revenge they have been searching for.
He is also worried about the Demon's plans for Sam. Before splitting up again, John dropped his bomb on Dean: either save Sam or destroy him... as John may not be around when the time comes.