It was all part of Discord's plan. When he got that trinket from Tirek, it was all over for him.
"Now I HAVE it."
He just needed something, anything that he could give to Twilight, and a good reason it was now a special thing.
And he's nothing if not a good actor... and a good liar, let's be honest.
I'm not sure if getting his own chaotic magic stolen was part of the plan or not. I sort of believe he did anticipate it. In which case, big props to Discord for willing to give that sacrifice.
Whether or not Celestia was privvy to Discord's plan, I'm not sure. You gotta think that wink at the end said yes she knew. Or maybe "I'll tell you about it later."
I'm surprised they left a few loose threads, though. Fluttershy's battiness for one... The Pony of Shadows for another. (That wasn't Tirek, was it? Nooo.)
I've got to think that if Hasbro knew MLP was going to last 5 seasons, perhaps more, they would have held off on the whole Princess Twilight biz for a bit longer. She really can't go back to being a regular unicorn now. And let's face it, being a princess an' all really does affect her day-to-day life.
Also, where can she go from there? It's going to get harder and harder to top each season opening/finale. Now that we expect these grand-scale two parters, they're kind of stuck with it. Just once I'd like to get a two part episode that wasn't all dramatic and spectacular. Can't they focus on the funny?
If they REALLY wanted to shock the viewers, they'd have her abdicate the throne sometime in the future.
Now I suppose we have to put up with another EG movie. It's cider season!
(Equestria Girls movies keep our franchise afloat between seasons!)