With the amount of newbie pc users who use this program, I don't think it would be a good idea to disable this check, the small annoyance to you is worth it IMHO.
And if you don't use the backup feature I hope you have another way of restoring the registry.
I know ccleaner is a very safe cleaner and I've been using "fix all" for years now, I still do the backup just in case.
Then clean those up every few months, it's not like they take a lot of room.