Terminology, maybe not appropriate, is one thing, reality is another.
How would any of you suppose that whatever software is able to “clean” a file? Maybe possible with some added data to a data file (e.g. Microsoft Word macros), but what about some dll or executable?
No software knows how to repair files of which it must be reminded that they are often hard-coded and copyrighted.
In these conditions, the only possible behavior is previous backup of the said files, and i remember that, speaking e.g. of windows XP, malicious contents also contaminate windows restore: you backup and restore sh…
The eventuality of some modern and working kind of sandbox, where all the “safe files” would be protected, would be a solution, but is not realistic unless one uses real-time backups on a different physical media.
This kind of technique, even if not using heavy hardware raid procedures, already exists, and supposes one has at least a full daily backup on two different destinations, in the same time he has protected rescue media.
Waiting for some hypothetic and utopic software to be able to proceed to automatic cleaning, the answer is clear: never allow whatever software to quarantine, clean, or delete whatever, knowing that you should not place yourself in a position in which this becomes an emergency, but letting you time to, manually, think by yourself about what you actually should delete.