Blanchy:

Perhaps the eyes are an opening into the body which increases the chance of disease and death. You would not need to increase the chance of death much to favor salamanders who lacked as large an eye aperture. After a while, perhaps the salamanders whose eyes had completely covered over would be favored.

Just throwing it out there.

That's quite possible. We're most susceptible to infection at our membranous surfaces, interfacing with the outside world. The eye is one of them. Why have this chink in the armor, if there is no function for it?