The eyes come back at the end of the poem when the examination is nearly complete. It will forever be blinded and deprived of its once perfect vision. Without its sight, the bird will conform, lost its individuality, and become like the surgeons themselves. In addition, some students started with a discussion of their stock response to the image of eyes in general. Let the text tell you what to make of the image, not the other way around.
Every inference drawn comes in response to something in the text.
Here the speaker is describing the surgeons actually holding the bird's brains in their hands, comparing it to a wasp's nest. This image suggests several things. First, it suggests the fragility of the brain. More importantly, though, it suggests the dangers inherent in Garuda's brain. This implies that the surgeons fear the bird in some way.