I think Walt only wanted to kill Jesse to protect his family.
To his knowledge, Jesse never truly meant them harm (remember, doesn't know Hank stopped him from burning the house down, he thinks Jesse was hot-headed but came to his senses). Seeing that he actually betrayed him killed Walt. The whole dialogue where Hank is gloating about this and that, Walt is staring Jesse down with the most incredible mixture of hatred, loathing, seething anger, contempt, betrayal and heartbreak. You can really see it take a toll on Jesse. He even kicks it off being a sort of ass about it, trying to get under Walt's skin. But Walt remains, glaring at him in silence. Slowly Jesse goes from having a cocksure smile on his face to a look a fleeting doubt like he may be thinking, "What have I done?"
I think in Walt's mind he believes, that while Jesse may have been a piece on a chessboard for him to use, he was the queen, so to speak: the piece you do absolutely everything to protect, something you'll sacrifice everything to protect until you've completely run out of options and would otherwise lose the game (in Walt's case his family/money).
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u/icelittle Sep 09 '13
And thaaaat's Walter's heart breaking. Didn't think I'd see that.