Since those whose ears the eels crawl into are subject to suggestion, might it not also make them more prone to violence? Perhaps it took just a few of those "infected" to kill a few other of their fellow supermen to come to that number, Or maybe one or two of those brainwashed were convinced for some reason to attack their compatriots. As tight-knight as Khan's group seemed I always envisioned the possibility of some sort of power struggle being possible in the years after they were marooned there, particularly after Ceti Alpha 6 exploded. Evidence for that possibility can be found in Spock's comments in "Space Seed" about the supermen being prone to fighting amongst themselves and how "superior ability breeds superior ambition". Maybe not all of them agreed with Khan's decision or leadership and tried to use the eels as weapons?
Then again, the eels killing off so many in the 15 years they were on the planet doesn't seem too farfetched to me even if they were aware of the danger early on. One would assume the larva are pretty good at "infecting" a host when they least expect it and as mentioned, Khan did say they died over time and death wasn't instant.
I think a bigger question is what makes the parasite decide to finally bug out from the host and what becomes of it? I always thought Chekov's earwig vacated because he was somehow able to fight it off by disobeying Khan, but we don't know if that's just the natural progression of it's cycle. Perhaps after having no need for the host when they reach a certain size, they then exit; the person dying of the trauma, Chekov not withstanding.
But just maybe once free of the body, they continue to grow and become an even bigger bugger; enough to be able to attack and kill the uninfected humans. If the adult eels were a few times bigger I could totally see those pinchers biting off heads. Maybe that could count for a few of the casualties, rather than all twenty being due to being "implanted". Then again, I wouldn't put it past some of those deaths being of other causes or hazards of the planet that had nothing to do with the eels. Remember Khan was a madman and made even more insane by his exile and just looking for someone (like Kirk) or something (like the eels) to totally blame for his problems; so I think some of the things he claimed or said could be taken with a grain of salt.