Depending on its current canonical status, it has already happened. In the Post-COIE retcon of the Legion's history, Superboy was revealed to have been from a pocket universe set up by the Time Trapper. Superboy then sacrificed himself to save the true Earth and his own. A pre-villainous Silver Age Lex then accidentally released 3 PZ Villains, who wiped away the world. Calling on True Superman to help them, the alt-heroes were still killed to a one. Superman used Gold K to depower them (it didn't affect a Kryptonian not from their 'verse). They then vowed to regain their powers, and one day repeat their crime on True Earth, taunting Superman as being unable to kill them. Finding their crimes abominable, and their threat a credible one (they had powers greater than his, when they had them) he exposed them all to Green K and watched them die. Several months later, a guilt-ridden Superman took on an alternate personality.
Well, as I said, its canon-status is doubtful, but it has been done before.