The Three-Minute Universe - Book 41 of the series, which I originally found by my search taking me here.
The Sackers may be the most hated race in the galaxy, so repugnant that their mere appearance makes most Federation citizens ill. That hatred runs both ways, and now the Sackers have stolen a powerful new device that they use to imperil the rest of the universe. They've torn a hole in the fabric of spacetime, an expanding tear so that one universe is leaking into another, and unless the Enterprise (TM) crew can stop it, it will consume everything in its path.
They are disgusting:
The Sackers were cursed with a physical appearance repugnant enough to turn even the
strongest stomach. In addition to their nausea-evoking exteriors, they gave off an
overpowering stench; most people of other races became violently ill in their presence,
vomiting uncontrollably until removed from the sight and smell of the Sackers. And to top
things off, Sacker speech was shrill and piercing, causing excruciating pain in their listeners'
ears. This standard response to the Sackers was purely a physiological one, and it couldn't be helped. But even after half a century of exemplary behavior, the Sackers still found that
their presence inspired reactions ranging from uneasiness to near-violent disgust wherever
They do indeed force Kirk to take command:
"We have need of your assistance," the newly named Babe told him. "Our ship has recently
suffered a disastrous accident. Every officer and crew member on the bridge was killed--not
one of our command personnel survived. I am a commander-in-training only. We brought
you here, Captain Kirk, because we need you to captain our ship."
From the book, regarding flamethrowers:
One of the two Sackers who'd stayed outside the refrigerated cell--the gray one--had a
weapon in his hand. Without further ado he pointed it at Hrolfson ... and set him on fire.
The plot twist is that the reason why the Sackers are acting so inconsistently hostile is that
The crew which kidnapped them are adolescents. All of the adults died in the accident, and the children are working off of a vague data entries on how humans act and react, and using equipment they're unfamiliar with.