Yeah, this is one annoyance with Altium. Then again, it's hardly consistent across other platforms. Going between Altium, SolidWorks, AutoCAD, and CorelDraw, scrolling, panning, and zooming all work slightly different in each one. After a while you get used to it and the muscle memory flips back and forth without too much trouble.
Using a 3D mouse helps somewhat--you should be able to set it up to behave the same way across any software that supports it, so it will at least be consistent across just about any other CAD programs you might use. Of course it means moving one hand off of the keyboard to navigate, so I still generally use the regular mouse to navigate in 2D, even though the 3D mouse works there as well.