One possibly solution comes to mind: While I'm not running an AL game, because my campaign is of an episodic nature, I decided to adopt the AL method of awarding "downtime days" as a consumable resource that can be spent on downtime activities in between episodes. I could make it so if he spends a certain number of his accrued downtime days, he can negate the penalty. He won't regrow his eye, obviously, but he'll be able to say he's learned to compensate for the lack of depth perception or whatever the mechanical penalty is meant to represent.
