Xlestia may have been planning to destroy their world, but even she did not deserve to be brainwashed by The Heartless before being turned to stone. By the Elements she once used to defend Equestria, no less.
Twilight's reaction to seeing her teacher corrupted and then turned to stone. That would be bad enough, but the worst part is she didn't even know Xlestia had made a Face–Heel Turn at this point and does not even know how or why the Elements turned her into stone instead of just cleansing her. Even worse, she now has to live knowing she is partially responsible for her teacher's fate without knowing why.
Also, Twilight having an understated Heel Realization after Sonic tells her about Eggman's Evil Plan to Robotisize the inhabitants of both worlds and saying just how messed up that is.
All the times when Xlestia got the rest of Equestia endangered/destroyed by invading a world where one or more residents turned out to be an Eviler than Thou.
In the SCP Foundation chapter, Xlestia has been captured by the Foundation following their shutdown of the barrier. While she was initially allowed to remain conscious under the effects of another SCP, she's since been placed in a medically induced coma and kept in cryostasis. Before being iced, she became obsessed with killing humans because the Foundation used an unidentified SCP to kill all the other ponies, leaving her as the Sole Survivor. The Foundation refuses to neutralize her because her abilities, not her continued existence, are what make her dangerous; as long as she never wakes up, she's perfectly safe for them to study.
Some of Xlestia's fates at the end of various chapters are... not pretty.
As Xlestia is about to finish her off, A.I. Celestia decides to Face Death with Dignity and spends her last moments continuing to serve humanity.
Bruce Banner's Inner Monologue during his attack on the barrier reveals that he tried to take the potion in a desperate attempt to qualm The Hulk. But when he realized the potion destroys all negative emotions instead of just weakening them, Hulk fought back.
