I love Fred. A lot. She is a great character and I like how no matter how much she grows, the show never forgets who Fred really is. I never had issues with how she went out, mostly because there was that one scene in the lab where she shouted how she couldn't let this thing take her, that she had to fight. And I think that basically sums up who Fred is. She's a survivor. My favorite episode for her is probably "The Magic Bullet" because it's basically her against the world, just like in Pylea, and she comes out on top, again.
She's the reason 'The Magic Bullet' ranks so high in my books.