You're forgetting the actual option was to do the titular "Annihilate". Kirk was gonna glass the planet to make certain the parasites didn't spread. The choice would have been "blind 'em or kill 'em."
On a somewhat cruel note---what an idea for planet pacification! As long as you're dealing with a species for whom sight is their primary way of navigating their environment, take maybe 500,000 or so people from the planet to form a ruling collaborator cadre, blind the whole planet, and then put your sighted agents back with maybe a few troops. Would be especially useful if there was some way to restore sight (at the least you could promise LaForge-style visors), you could hold that out as a possibility for the billions of blinded and most of them would probably do ANYTHING to be sighted again (so that you wouldn't have a planet of only useless wards for the rest of their lives).
I can so see the Terran Empire doing that. The Dominion, too.