Reg: Keeping the dead, dead
Why bother?
Use a Magic Jar spell to trap the bad guy's mind outside of his body, place said gem inside a chest particularly Draumaji's Secret Chest, send it off, kill said bad guy's body cremate and then spread ash into a volcano for good measure.
The first wish can only recover the body even try to return it to life but it won't restore his mind since if the party keeps it quiet a second wish MIGHT restore his mind but given the spell keeps the said chest on another plane there should be a good chance this will destroy both chest and gem holding his mind and an even greater chance they won't be in any condition to get back to their normal evil selves... by all rights the GM would be better off conceiving of another way they can get back but thats another story...