After all the Tim Donaghy stuff, if there's any intentional refereeing bias in the league, I seriously doubt it's coming from Stern. You could probably make a case that Stern still favours the larger market teams to stock up on stars though.
But some things never seem to change in the way the referees call a game. Melo for example doesn't get the star calls because he has the perception of a whinger. Sheed got ejected yesterday because he has history and the refs know that.
What I'm getting at is I think the referee bias is more from perception of some players rather than any mandate that certain teams should be more successful. Otherwise New York wouldn't have just suffered through the last 10 years.
Stern cares about his product now, he doesn't care that Pop is resting his players for a playoff run, he cares that Pop sat his 4 best players in a nationally televised game (incidently, one of the most watchable games of the season so far).
If the idiot had just waited til the next day to make a statement, he could have commented on globalisation of the game and how he has shaped that product, but because he rushed in and said there'd be fines, he didn't have a choice but to fine the Spurs.