One good reason is that if you remove something from a jar, you risk breaking dependencies of other classes in the jar. But, I agree that this is babying a user who may know what can safely be removed.
You can work around this easily enough by renaming the jar to a .zip file and manipulating it with your favorite .zip editor (Windows File Explorer will do this). Rename it back to a .jar when you're done. Jar files use standard zip packaging and compression...