I don’t see any files being served from this plugin on your site currently. Can you elaborate on what you mean by “messes up”? Are any error output? Is it just the display of things not working? Does the Javascript console show any errors? Once the plugin is deactivated through WordPress none of the files in it can execute by design of WordPress.
My only thought is that you have another caching plugin installed too and that the html that was loading the files was actually caching the paths to the mncombine plugin files? Do you have another cache plugin installed?
Anyway, it looks like there are no references to the plugin at all in the source anymore and you should be able to remove the files placed in the mncombine folder. Save them just in case. If it does mess the site up again once you move them maybe you can let me know so I can take a look again real quick. Thanks!