Apple released macOS 10.12.1 this week. It appears to fix the problems with sensitivity of scrolling with an Apple touch device.
I have just installed the update and tested scrolling to zoom in the Composition, Layer, and Footage panels with an Apple Magic Mouse, and the behavior now appears to be the same as on 10.11.6.
Also, as I mentioned above we investigated disabling scrolling inertia when zooming in the viewer panels in After Effects, and I'm happy to say that in the next version of After Effects this will be the case. This change makes the zoom behavior feel predictable with Apple touch devices, and eliminates the problem where accidental swipes or too-quick-flicks of your fingers cause the viewer panel to zoom all the way in or out. (Accidental swipes or flicks, if they happen, will still zoom the viewer. But now the zoom amount is based on the distance you move your finger, same as a mouse with a physical scroll wheel.)