Classloaders can be a tricky problem. You can especially run into problems if you're using multiple classloaders and don't have their interactions clearly and rigorously defined. I think in order to actually be able to unload a class youlre going go have to remove all references to any classes(and their instances) you're trying to unload.
Most people needing to do this type of thing end up using OSGi. OSGi is really powerful and surprisingly lightweight and easy to use,