As far as destroying Skynet goes, they only got the one facility. John's voice over at the end talks about how Skynet is still in control around the world. They have facilities all over the place, so it is still there to be the driving force for future movies.
The T-600 didn't ripe out the prototypes heart. It just punched him in the chest right over the heart, which caused the heart to stop. John was then able to get the heart going again. The prototype is different from the T-600s and T-800s because of the organs...He/it needs the heart to be beating to stay functional. That's why he was just laying there until John used those cable things to shock the heart back into beating.
