Fluttershy promises not to use her element against Discord and because of this, Discord thinks he's won. However, Fluttershy's element is kindness which means she was bombarding him with her element the entire episode and it ultimately defeats him.
As a reality warper, there isn't much Discord could lose that he couldn't just replace. Except a friend, apparently.
Fluttershy had proven in their last meeting to be totally immune to Discord's manipulation, to the point she was the only one he had to brute-force mind control. Since that's not an option here, he never had a chance.
