Though this is an old question, there is indeed a way to replace the system ClassLoader.
You might get more than you bargained for, however, with reflection.
Field scl = ClassLoader.class.getDeclaredField("scl"); // Get system class loader
scl.setAccessible(true); // Set accessible
scl.set(null, new YourClassLoader()); // Update it to your class loader
This should work on the Oracle JVM.