How many times have you had to abandon a refactoring exercise because you can't check something out or regretted doing it after spending days blocked in a merge?
Eclipse, or any other modern IDE, should be able to let you refactor hundreds of files in one go. But most projects would shy away from any such change, preferring to work in an imperfect world than face the project disruption or ensuing merge hell.
I don't like it when support tools like CM, invaluable though they are, have a direct influence to the project implementation. Which is why this article came about. It tries to solve the issues of using archive files as the unit of control, albeit with a step back in technology.
Using a higher level of source control produces some benefits that may tip the balance. Things like consitent checkins, build script simplification, one source one jar etc. But these are more conveniences, the main gain is in allowing the refactoring to take place unhindered.