They cut it to tell a very different (and misleading) story. To Firefly fans it'll probably feel off-kilter, but to those new to the 'verse it'll probably be more easily digestable and appealing. All in all it's probably a good thing. Show the public what they think they want (basic supergirl shoot-em-up) and deliver something more complex when you've got 2 hours worth of their eyeballs.