Long story short, the model geometry that you see is different from the collision geometry that we use for hit detection. The Elite's collision geometry is tighter than the Spartan's, compared to the render geometry, and the old headshottable region was halved in size.
The only objectionable side effect of this is that shooting an Elite in the kisser won't actually be a "headshot" (you need to hit him higher on his head). But I don't think that's going to be an issue in anything but laboratory conditions.
It'll never be perfect, but our goal was "close enough that you felt like you actually had a choice in casual play". I don't expect MLG will be using them any time soon.