Just killing (or capturing) the boarding party would not suffice for Kirk. He had a helpless starship while the Klingon commander had a threateningly armed one. Kirk needed to negate that threat somehow: either the Klingon ship had to be destroyed, or then captured, or then deprived of targets.
Destroying the Klingon ship by conventional means was obviously not possible. Boarding would have presented quite a risk, too: Kirk had no real idea of what sort of opposition he would face, but he did know he'd have to drag the less than combat-capable McCoy (and Scotty) along for the fight. Trying to blow up both ships would have been a pretty clever move, and would imply that the scuttling did not go quite as planned since Kruge managed to escape. Just blowing up the boarding party helped already, though - but escaping from the doomed Enterprise
was a necessary move no matter what, so stun gas or containment fields would not have been viable options, as they would not have diminished the Klingon fighting strength and ability to hunt down Kirk's party in any way.