Your Empire is a dieing beast that allows those damn elves to torture and kill innocent worshipers in their own homeland. A true new Empire shall raise from the ashes of Skyrim's Civil War with blood of the Dragon heralding into life. Those damn elves think they can destroyed Nirn by killing off humanity.
Humans can breed much faster then elves. Skyrim's population can recover and maybe this new generation will be taught the Voice? Plus, secretly killing off one elf at a time most hurt their numbers too.