It was not what was originally intended either. John was supposed to be an abusive and paranoid alcoholic, but either the network didn't want to be so heavy handed or else Jeffrey Dean Morgan had more clout than expected in the role. I remember that he said at some point that he didn't want to return to the show because he didn't like what they had done with the character (in his absence). Little wonder that when he did it was a very surface sentimental sort of thing. However Dean and Sam were also meant to be more at odds in S1 but the bond between the actors overrode a lot of that, plus so much of the show was simply done on the fly with no thought to long-term planning.

Speaking of that and analyzing what was intended, I wrote about the original pilot draft and you might find that of interest: https://archiveofourown.org/works/6768631