After Spock beamed over the torpedos to Vengeance, should he have
I think the last thing Spock wanted was to get more of Khan's attention on the Enterprise.
He had no idea what reserves Khan had at his disposal. Khan had designed the Vengeance hadn't he - he could have lots of unknown Section 31 gadgets hidden away. He'd already threatened to kill everyone aboard the Enterprise to get to his people. The Enterprise was in enough trouble.
And frankly (I'm a horrible person I know) didn't care that much about random people killed in San Fran by the crashing Vengeance. After all I didn't know any of them.