I also doubt that Aunt Lydia feels guilty about Janine's eye.
As with Commander Putnam's hand, Gilead believes this sort of thing is not so much a punishment as an opportunity to repent.
When the Commanders were discussing what to do with Putnam, Fred was pushing for leniency and one of the others said his wife had already been in to plead for him. Fred thought she was asking them to be lenient and the other Commanders said something like "No, she's asked for the full penalty of the law. She really loves him." And then they took his hand off.
Aunt Lydia will see taking Janine's eye as the steps necessary to bring her to God.
Which is basically hurt and terrify someone so much they go crazy but become easier to control.