Celestia banished Luna to the Moon, where Luna spent a thousand years alternating between being insane, breaking free to suffer crippling depression over the futility of her life, and then being tormented by the Shadows to weaken her so that they could resume their possession of her. Now, Celestia didn't know that the Moon had been overrun by exactly the same entities who had made her Nightmare Moon in the first place. But the result in any case was that Luna suffered incredibly, something Celestia would have been horrified to know she was doing. And of course when Luna returns, Celestia knows some of what happened. The worst part? Celestia had no other good choice. She didn't have the power to purge Luna alone, and she couldn't let Luna kill her or devastate Equestria.