I think that you may be able to change this without changes to PDFNet.
Did you try to attach your own MouseWheelEventHandler to PDFViewWPF.GetScrollViewer().Content?
GetScrollViewer() returns standard WPF ScrollViewer:
http://msdn.microsoft.com/en-us/library/system.windows.controls.scrollviewer.aspx
PDFViewWPF attaches its own handler to
PDFViewWPF.GetScrollViewer().Content.MouseWheel += new System.Windows.Input.MouseWheelEventHandler(this, PDFViewWPF.OnContentMouseWheel);
so I assume that you can do the same to override the default behavior.