I'm pretty sure Pete was supposed to leave the series when he did and it wasn't because of contract issues. The entire story was built as Clark having everyone he knows betray or leave him, thus giving Pete the perfect window for leaving, especially after getting the crap beaten out of him during most of season three.
That super leap by Clark on to the nuke was amazing. The new opening credit sequence kicks ass, too. The old one was so bad that I actually could have put it together myself if I had the footage.
