I don't really see a problem here, either way. Each character (PC and NPC alike) was acting to his or her personal dictates in a reasonably believable fashion. Deciding who was 'in the right' is too campaign-specific for anyone outside the game to really adjudicate, IMHO, though clearly at least one of the PCs and the DM have a disagreement about how such social interactions should work.
Kahuna Burger throws out certain medieval precepts, which is fine and quite reasonable (especially given how historically inaccurate D&D generally is). In her view, if I read correctly, social rank is not nearly as significant a factor in-game as it might be in someone else's game, such as Fenes, who expected the NPCs to be much more deferential. Certainly this is more a question of style. I don't see a 'correct' answer to the question of how either the PCs or NPCs acted in this situation.
We don't know a LOT of details about the game, the campaign setting or the characters involved. And it's possible that the players and DM themselves have never hashed these details out. Part of the fun is discovering them, for some folks.
I think it's safe to say that the cleric who was wind-walking made a tactical error in approaching the keep in wind-walk form. Certainly, it wasn't beyond reason for the militia to attack a mysterious cloud creature. Sure, it claimed to be one of those hired adventurers...but it could turn into a ghostly cloud-form; could shape-shifting truly be beyond it's capabilities? Could it be some new form of undead? The expectation that a guard captain in some remote barony would be an expert on the living dead strikes me as a tad remote. Firing first and asking questions later? Not a bad call, necessarily.
So the real issue is that the guard captain was a JERK. Then the PCs, one by one, back him socially into a corner, and like any cornered animal, he viciously bites back. He is defensive and rude to his 'betters' (which contextually could be more capable warriors or socially more endowed characters) and when challenged and berated for doing his job (from his perspective) he becomes churlish. When challenged, rather than look weak before his peers, he stupidly accepts a duel he knows he cannot win and is soundly humiliated. His men, seeing this, take it as a personal insult and in the name of solidarity decide to wait out the next attack bolted into a secure room to allow the (to them) self-righteous outsiders take care of the heavy-lifting by themselves. We've been told that the village has already had refugees flee the town, so it sounds like they're really only holding the keep at this stage...so they're not shirking their duty.
From the PCs viewpoint, this played entirely differently. They expected that once the guards were informed that there was no threat, that they would nod, apologize and move on with the duties of the day. When the guard captain, already on edge, reacted with attitude instead of contrition, they found their authority and potentially their misson threatened. When the warrior (Maugrim, was it?) came out and found the guard not only being rude but being insulting to a member of the nobility, he took personal offense. They quarreled and the warrior decided that the commoner guard needed reminding who his betters were; losing his temper, he rashly challenged the guard...and then soundly defeated him handily. By this point, he regretted his choice of actions...not because the guard didn't need a good thrashing, necessarily, but because he wished that he could have solved the situation in a more satisfactory method other than humiliating the captain in front of his own men. His conflict comes from the realization that he has failed to show some of the qualities of a leader that he had hoped to display, but found the guard intractable to the point that he was left with no other choice, due to his own social customs.
Again, I don't see a real problem here, if I've sussed this out even remotely close to what happened. The only real issue would be whether or not the players and DM agree as to the assignations and motivations and their relative goodness. (and for that matter, how the social chain works in his game). All of this assumes that the situation could have been resolved differently...and it's possible that it might not have been. The guard might have accepted nothing short of magical compulsion to behave a certain way...and that's, IMHO, fine.
To me, this sounds like a good role-playing situation, honestly.