Draft picks aren't much help when you're competing for a championship right now. There are two things owners/franchises are always trying to do in the NBA: Win a championship, or make more money. This trade doesn't help them win a title, so it's an odd move for them to make. If I were a Thunder fan right now I would be annoyed.
I understand that perspective, but I bet Presti knew that the Thunder just couldn't match up with the Heat with their current lineup. Harden was a no-show in the Finals and never brought strong defense to the table. The Thunder are still VERY young and can look mighty strong if Lebron/Wade/Bosh become too costly to keep together in a few years.
The 16ppg Harden provided can easily be filled by a few other guys, and if they keep cycling through draft picks they can have that done on the cheap. Durant, Westbrook and Ibaka aren't gonna get cheaper as they re-up down the line. The max they can sign will grow each time around, making Harden's pie more and more punitive. He is clearly not at the skill level of Durant, nor the talent level of Westbrook. And in the NBA, a big like Ibaka is worth more than a 6'5" SG.
They do need to do something about Perkins though. Amnesty or trade, either way he was just as useless in the Finals as Harden, and his contract (though not huge) does limit their flexibility to sign veterans looking to chase rings on the cheap.