Have you taken a look at Aperture's preferences to see, if one can set the scrolling speed there? Maybe you can also adjust the scrolling speed/distance via System Preferences > Mouse/Trackpad.
I don't see a preference for setting the scrolling speed in Aperture, but there is another scroll option next to the main scroll bar. With that you can scroll at any speed from slow to very fast. It's not as convenient as mouse-based momentum scroll though. I would suggest clicking on Aperture > Provide Aperture Feedback and let Apple know that you'd like to be able to configure the mouse-based momentum scroll speed. This is already an option in System Preferences > Mouse, but it clearly doesn't apply to Aperture. Perhaps the better suggestion would be to have Aperture respect the scroll speed set in System Preferences.
I have the same issue. My mouse is a Logitech MX1100 with a free spinning scroll wheel. In A3, I need to lock the button to click mode to keep it from jumping around, even after I select an image. I have taken to using the arrow keys to move through the library. It's easier and more accurate. An addition to the Preferences that changes scroll speed in A3 would be nice. Also something that locks the selected image until it is deselected.