It would make much less difference in baseball, assuming the unbalancing wasnt extreme. Baseball plays 162 games, Football 16, so, a few games against better opponents for the better teams... sure. Lets say:
15 games against the other League
60 games against the other 10 teams in your league
An additional 12 games against the teams that finished in the same place in the other 2 divisions
75 games against your own division. (3 teams with 19 games, 1 with 18)
I would do that, but I am not sure how that is relevant to what I said. The difference in strength of schedule is minimal. The unbalanced schedule is not what makes football more balanced, it is partially the nature of the game (football is much more contingent on team play, 1 or 2 weak positions or key injuries can crush a team, where baseball is more individual based).
My point was that you can trade draft picks and still be balanced. You just need to restrict the "cash out" abilities of teams to flat out sell draft picks. If that was going to be a problem, it would already be one with poorer teams selling prospects, but the league already intervene's if a team tries to do that. There are ways to restrict draft pick sales so that they can be forced to be somewhat balanced.