My guideline in raising kids is that consequences must feel "natural". That is, the kid must not consider feel punished, but feel like that whatever hits it after it had done something "wrong" is a natural, physically deterministic consequence of what it did. Retribution has no place in this. If you cannot undelete what you have deleted by having something precious to destroyed, then why destroy something of yours in the first place? (Of course, that's the ideal, and I openly admit that sometimes I do fall short of this. But still, it is how I strife to do things.)
In the case you mentioned, where the destruction was done accidentally, the first consequence I can think of one "natural" consequence: "If you are not yet experienced enough to avoid such fatal mistakes, you cannot use the machine on your own. Someone has to be there and supervise your interaction, and that someone has to find the time to do so."
That will seriously limit the amount of time the kid can use the machine, and thus be a punishing which teaches a lesson. Yet it will feel "natural" (if explained as such).