OK. And she may want to emphasize that, but the pirates do not see her as a command figure, but as a Knight.
Also, I don't think the current characterization of her is so out of line. The pirates will certainly notice that nothing in her oath mentioned either commanding with benevolence or actually obeying orders. Khem is trying to do right by her and by the fleet, both. Ii probably would better fit the role of engaging foes as she chooses instead of acting like a commander. The pirates will best accept her in that role; if she tries to take command more explicitly, there are bound to be problems.
Speaking of problems, so far you haven't even started to deal with the REAL pirates, the graith of the fleet.
I have been in command, albeit it was a unit of about 6-12, but I have had command in my previous rank, that's why I am a "Sarth’Gar", aka Lieutenant.