While I'm also not a believer in NBA conspiracies, the whole OKC situation is troubling.
Stern and Clay Bennett are great friends. To me, that's a conflict of interest. I don't think a single second that Stern is giving some kind of instructions to help Thunder but the human nature pushes NBA employees to please their boss even without realizing it.
When Abaka punches Griffin in the nuts and isn't suspended, I can't rule out that the NBA discipline committee had in their mind "let's not be too harsh with Abaka because he is a member of the Thunder, a franchise our boss likes".
It's the same thing with some NBA refs, they know they are being constantly evaluated and that if they make an error in favor of OKC, it would be less a problem that an error in favor of Spurs because Stern likes OKC.