While the .jar file that JavaLoader uses itself does get locked down (I know.. I can't do anything about that one), but .jar files that you use with JavaLoader no longer are locked by the system!
To note, the JavaLoader cfc has had one of its arguments removed - 'loadedClassPathBias', simply because it was more difficult to implement with the new code base, and there didn't seem to be a case for it. By default,JavaLoader will load the specified jar files before it loads the parent's, if it has one. Honestly, I don't think this is going to affect a single person, because I would be shocked if anyone actually ever used the option.
Please note there are some issues with memory and JavaLoader, so make sure you put your JavaLoaders in the Server scope. See here for more details.
If you find any issues, please post to the forums, or contact me directly.