Quickclean is merely a tool to do what you can achieve using Windows own tools basically. It used to be a seperate entity and was more powerful but now is intended only as a sideline utility to the major components - a "Lite" version. It is by no means meant to function as a fully-fledged registry cleaner.
Personally I don't think it's wise to use registry cleaners in any case as they eventually remove vital components, it's just a matter of time before that happens. All the cleaning up you need is emptying the Recycle Bin and using the Control Panel > System & Maintenance > Disk Cleanup.
In my opinion registry cleaners have their uses especially if you try some piece of software, don't like it and you've done a windows uninstall. The registry cleaner will remove the info from the registry, which windows will not do in some cases.
I have another registry cleaner, which cleans the registry however ,somehow Mcafee quickclean first will not do the same and somehow retains the information on the registry changes.
The issue is not on the importance of the registry integrity, whether or not you can speed up the machine or if it is safe to delete registry entrees or not.
You said that it is a minor tool in the overall program, and that this tool has been downgraded. There is no information anywhere that Mcaffee for the purpose of overall windows safety has removed the functionality.
The real issue is, as a customer it is quit obvious and logical that if this portion of internet security is faulty, that it is reasonable to doubt the integrity of the entire program. Especially after doing a complete nuke and pave. And it further questions the integrity of the my account you have on a re-download.
Well I'm only a volunteer here, Technical Support Chat may be able to give you a more concrete answer.