If Microsoft has even a shred of sanity, they would have defined the
basic mouse interface that all mouse companies must implement.  The
vendor might extend it.  Switching left and right can be done so
easily in software, surely it should be part of the standard API.

The problem is every OS would have its own mouse driver interface, so
you have to resolve the problem separately for Linux, Solaris, etc.

Java Web Start has a neat feature to use the correct jar full of
native code for the given platform.  Your program does not need to do
anything to select the correct code.
http://mindprod.com/jgloss/javawebstart.html