Eh...I don't buy it. Walter may like Jesse, he may feel sorry for Jesse, and he may feel responsible for Jesse, but starting a drug gang war isn't going to be very healthy for his family or his cover story, and Walt would naturally put his family first. Is Walt secretly in love with Jesse or something? That's the only way this rather unexpected plot twist works.
The writers just did it because they need to up the stakes for the season ender, not because it makes any damn sense!
Jesse is emerging as more interesting than Walt, despite being a four-star hypocrite. He's enraged about his friend, disgusted that children are being abused, but he apparently is oblivious to the lives destroyed by his meth. Silly boy.