Cyclone's overriding is pretty important for importing Max files. Without it I wouldn't have been able to port the RTC library that fast. Of course porting RTC involved replacing many objects with their Pd equivalents (and being a pd-vanilla fanboy, I mostly used builtins and abstractions for that). Other users may be fine with keeping Cyclone loaded and run the Max originals - freedom of choice is fine here.
If freedom of choice is a goal, then maybe the behavior should be user-configurable with a flag, allowing one to keep builtin names and use aliases for any conflicting lib classes, OR use the lib's class names and make aliases for builtins. Either could be the default as long as it's documented.
Matt