I guess I'm missing something here. You said that the owner receiving Santana was giving up nothing to receive Johan? Couldn't that owner essentially do the same thing the Pujols owner would do with Utley? In other words, if the trade didn't happen, that owner could keep 5 players and redraft Utley as the #1 overall pick, essentially giving him 6 keepers. If he had any value at all in the later rounds, I would bet this owner ends up with a really good roster after the draft. To me, that would be the value that he's giving up. Plus, it seems clear that the #1 overall pick in your guy's league is a hot commodity, so this problem should have been addressed when those rules were put in place. As far as breaking any of the rules though, I don't see where their trade would have violated anything. I'd be curious to know why so many of the other owners voted against it also. The number of picks in all rounds remained the same, assuming the player receiving Johan loses both his 1st (Johan) and 2nd (Utley) round picks.
The second point of your argument is a good one. That example, IMO, would be eliminated because the league/ commish would veto based on collusion/ cruel intentions, even though it would be allowed by the rules.