Yeah, that's right. Half-orcs should have an ECL of -1 because they make lousy wizards, bards, and sorcerers. Dwarves too, because they have that Cha penalty - n fact that hurts them as clerics or paladins as well. Oh, gnomes and hobbits aren't good fighter-types because of the Str penalty so we should lower their ECL too.
(OK, sarcasm over.)
Yeah, a centaur Wizard2 isn't going to be as good as a Wizard10. But you know what? You're making the wrong comparison there - it's like saying that a Fighter8/Wizard2 is clearly not 10th level because he can't cast as many spells as the Wizard10. Of course not! He's got other things that make up for it. So does the centaur. Like huge stat bonuses: Str +8, Dex +4, Con +4...
Sure, the centaur's not the optimal choice for a wizard. But to balance things correctly, you must look at the optimal choices - otherwise, when people take those optimal choices, the characters will be too good.
J