I wouldn't be surprised if Twilight becomes corrupted somewhere along the line of FiM's run. Something that is very noticeable this season is the recurrent theme of dark magic, in 3 out of 5 episodes so far. In the second part of the Chrystal Empire special, there's a scene where Twilight uses for the first time dark magic. Though taught by Celestia, this brief moment can be a critical hint that Twilight is not far away from a dark magic takeover.
To add, we all know that she's getting stronger and casting more powerful spells. This will surely make her more desired and attractive for any evil, cunning force that either sees her as a threat or as a valuable acquaintance...