I do not see why could not a official faction be held responsible for the behavior of this captain.
The report could have been what it is, and then the captain would be summoned to explain himself. the LN Should be keen on believing the gunboat captain instead of the unaffiliated mercenaries so basically unless he's really dumb he would have gotten away with it.
Sadly he taunted you what sucks, and he would probably get a "shape up man" notice but should he feel that trader is more safe with him he surely can take away your job.
Police should be able to have bigger authority than civilians, official faction or not. The problem is what happens after the first person reports him to the high command.