IIRC, the PILOT was in the can, and "leaked" to the internet.
A lot of changes have been made to the show sice it was made.
As for the whole "organic matter" thing - I wondered why Arnie didn't bring some weaponry in his chest, or even use the aforementioned pig-plan way back in the 80s.
The A-bomb, I suppose, would be a bad idea because Skynet would obviously want to kill Connor, but make as few other changes as possible, just in case it somehow destroyed itself by changing another aspect of history.
Lastly - Why the hell wasn't Officer Austin played by Robert Patrick?