So do you know or do you not know the Apple ID that is signed in to iCloud?
If you do know it, and its password, then you can sign out. You cannot have it all hooked onto one ID and have a different passwords at the same time.
You cannot have it both ways. They are either the same account, or different accounts. you can't have one account with 2 different passwords.
Also signing out does not in any way remove any credit balance you may have on your account. You can sign out of the account and its associated balance will remain with it. It does not get wiped out.
If the account logged in to iCloud is different to the one you use for the App Store and the iTunes Store, then logging out of iCloud will have no effect on the other account whatsoever.
If its the same account as the one logged in for the App Store and iTunes, then logging out will still not affect the account or its balance, it will just be logged out of iCloud.
If you do not know the account that is logged into iCloud, then you will need to wipe the Mac to remove it. This however, would have nothing to do with what account you use for Software Updates.
If you have a mess of accounts with different ones logged in to icloud, associated with the operating system and apps,
logged into the store etc... Apple did not cause this, and there is nothing they need or can fix.
Instead of automatically blaming Apple for something you caused, perhaps understanding how it works and how it can be solved would be better.
The first thing to do is to understand what accounts are signed in where.
There's 5 different paces an account can be signed in on a Mac. iCloud, Mac App Store, iTunes, Messages, and Facetime. The Apps themselves can be associated with an account, this is generally the same one used with the Mac App Store, but can be a different one if they were downloaded with one account, but then the account for the Mac App Store was changed to a different one.