Now, see, I take the "only indigenous lifeform" line to mean that their entire species survived. What Khan has is just a small sample of the eels that remain.
Further, I always assumed that the eels didn't attack the Augments until after the explosion of Ceti Alpha VI. Before the explosion, the eels had their native/indigenous food source.
Well, this is more or less what I assumed when I saw the film, too. The question is, though, given the collapse of the ecosystem, what do they eat?
It makes me wonder just how many other indigenous life forms in truth also remain.
"Life form" has been applied inconsistently in Star Trek.
Often it is used in unqualified form to mean a sentient, if not humanoid, life form. Kirk and Spock stand in a grassy meadow, and Spock says, "Scans show no life forms on this planet, Captain."
Sometimes they got it right and said something like "no animal life", except just don't pay any attention to the entomophilous species.