Seriously, why does everyone think that this is a bad idea? I don't understand why anyone would call this a butchering of the show, it certainly fits in with the overall direction Twilight's character development has been going in.
In the very first episode of Season 3, when Celestia was explaining to Twilight about the Crystal Empire, and how she would reach the "next level of her studies, we see this image:
We know that it's going to happen, it's been forshadowed. And despite what you might think, it won't be the end of the series, because Season 4 has already been confirmed.
Furthermore, the writers of the show KNOW VERY WELL WHAT THEY ARE DOING AND WON'T SCREW IT UP.
Remember Princess Cadance and Shining Armor, and the backlash from their initial introduction? Twilight has a brother? There's another alicorn princess? Everyone practically screamed that FiM was RUINED FOREVER.
And do you know what really happened? An awesome season finale, arguably the two most intense and exciting episodes in the series. People loved it. And odds are, people will love the season 3 finale as well.
EDIT: Changed the thread title slightly.