Personally, I think it would be safe if you are safe yourself and go slow. It takes a shock to set off a primer. I think you would just crush the priming pellet and the primer will pop out like a used one.
Very important: by being "safe yourself", I mean wearing safety glasses (you always do anyway, right?), and perhaps a face shield and leather gloves. You never know what might happen. Also I would crank the depriming pin down as far as possible and still have it centered. That will assure you of having some air space in the die.
All that being said the safest way to solve your problem is to fire the primer in your gun and then deprime normally. I wouldn't try to make the primer inactive by pouring something on it like WD-40 or oil, etc. That would leave a residue in your cases that would be hard to remove and might affect any new primers.