I think it was Hydreigon who tore Ghetsis's eye, maybe 'cause the Plasma Leader forced him to evolve early using bad methods,or even torture. So Zweilous evolved,but as a redress he tore apart that poor eye. It's a popular belief this.
I can see the eye damage coming from the Hydreigon family line. But still, how he is in White 2 and Black 2; using that poke'ball signal canceler as a can, where he needn't any support in the previous games, kinda says he got injured even more. Now whether that was still his Hydreigon, or Kyurem before he gained control of it, is up to debate.
But you have to consider that Ghetsis is a cold man. I wouldn't put it past him to use brutal methods to control his Pokémon. We thought that Cyrus was bad with his indifferent nature and Giovanni for creating Mewtwo.