Fortunately, I’m wearing my yellow shirt, not my red shirt.
Gotta make a correction.
The Enterprise does fire a torpedo at God when (or shortly after) Sybok is grappling with him/it. The Enterprise crew had a bit of time to run away, so they weren’t exactly right in the line of fire, but they were kinda close. The torpedo blows up the stonehenge-esque thing that grew up out of the ground.
So, the Enterprise does fire a torpedo, but the scene in which Kirk just barely gets shot is with the Klingon Bird of Prey.