One must wonder why Iai Bancho didn't just CLOSE HIS EYES, especially since he closed them anyways after slashing them out. Might be Rule of Cool and Honor Before Reason mixed together...
Speaking of Iai, when did his eyes get better? He's injured one arc, wears bandages the next arc, and is back to normal the arc afterwards, with no explanation.
Possibly he only cut enough that they could not open, hence the healing and closing beforehand. On the other hand it may simply be the Banchou standard Regeneration coming into play.
They did state way back in the early chapters that many Bancho have undergone experiments or augmentation to gain their unique abilities. A healing factor might not be out of place. In fact if you surmise that the elder Kongou is a product of earlier experiments and his sons Akira and Takeshi are super prototype versions of the next model of augmented human it does not come as a surprise.