The MLB site has an article that is purportedly "not subject to the approval of Major League Baseball or its clubs." But it does closely mirror the spirit of Kevin McClatchy's sentiments. Maybe he's just a big fan of the site.
The article does contain the one valid argument that I've heard/thought of against the existence of collusion:
"If collusion is afoot, somebody forgot to tell, for instance, the Yankees, the Mets, the Phillies. They haven't been colluding very well, what with those hefty free agent signings. Your basic collusion generally requires 100% participation to work. Partial collusion would not be a particularly viable, even scary, course of action. "
There are caveats even here. The Philles are moving into a new stadium in a year and have grossly neglected their team for years. Perhaps they were given a one-year pass. The Mets have cut some high-salaried players and are trying to cut still more, but are also competing with the Yankees. Given the dislike that the Selig loyalists have for George Steinbrenner, the Yankees could have been kept out of the loop in order for the others to exploit them come welfare time.
I'm not making excuses to promulgate the existence of collusion as if I have conclusive proof. I'm just saying that scenarios can be constructed to explain these apparent outliers. It makes the whole collusion thing more complicated, but given the surreptitious nature of these alleged machinations, it is not entirely impossible.