Emanski is correct. If the Commish tried to change the draft rules, the MLBPA would file an unfair labor practices complaint with the NLRB and get it enjoined. The current players are not necessarily willing to bleed for the guys who would take their jobs, but they don't want management to start thinking it can make changes to anything in the CBA without the union's participation.
There may also eventually be some realization that, the more expensive prospects get, the more established players can command, due to the effect of comparing one to the other. If the union were smart, it would oppose the slot system. But what I read is that they would likely give away this particular chip as part of a negotiation over more hot-button issues.
Look for serious changes, but not until 2012.