"Kill" is the wrong word. I think it was more to drive it off long enough for the Klingons to beam Kirk aboard and get away. Once clear of the surface, the entitiy would seem to not be able to really effect them.
Also the torpedo was likely low yield as not to kill Kirk.
I was always under the impression that the entity was, to your point, just forced to retreat by the disruptor fire for long enough that the ship could escape back into orbit.
What do you think the being meant by saying "bring the ship closer so that I might join with it?" That's kind of an eerie, cool thought.