The big question you needed to ask yourself Az005 is this...
"When the PCs bring the refugees to the gate of the city and the guards don't let them in, what should the PCs do?"
Because unless I've missed your explanation in some of your reply posts (which is quite possible) I have not seen what you had in mind for the answer to this dilemma. Did you have one? Did you have in mind at least one "right action" the PCs should have taken? Because if you didn't... then you can't blame the PCs for not thinking of one either, nor question their actions for all the ideas they came up with.
Bringing the refugees into the city was not an option in your mind, turning around and going back the way they came was not an option, abandoning the refugees outside the city walls was not an option, and disregarding the guard's commands by sneaking them into the city was not an option.
Now I understand completely why these were not valid options in your mind (NPC guards were controlled; army was advancing; goes against alignment of good; goes against alignment of lawful-- respectively) but at some point if these were not being allowed on the table without grave consequences for doing so, then you as a fellow improviser need to offer up some other 'Yes' options to them to possibly take that doesn't result in these grave consequences.
Now some DMs would be quite happy with presenting this "no-win" Kobayashi Maru scenario and then letting the scene play out. The PCs hang themselves with whatever option they take and the DM accepts and smiles happily while the PCs chew him out for screwing with them (some DMs actually get off on that, believe it or not)... but it sounds like this was not something you really wanted to get into. As you say, you were going to be yelled at regardless. So the question becomes what are you going to give them that gives you what you both want-- the PCs depositing the refugees safely and completing their task; you throwing up a dramatic conflict that the PCs solve. And for that... something in your mind and your plot has to give. It's hard as hell to allow yourself to do that when nothing the PCs do seem to make "sense"... but if your optimal result is the PCs solving the problem without you getting yelled at... either you give them the breadcrumb clue to solve the problem your way (if you have one), or you allow this one time of breaking what "makes sense".
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And BTW - as one final caveat and recommendation... never use game mechanics as a decision point when it comes to roleplaying. Just because the game mechanics say that the Trip action is much more deadly (tactically speaking) than hitting someone with a sword... this is in no way true from a roleplaying perspective. The reaction a town guardsman would have to seeing someone stick their foot out and trip somebody would be much, much less than seeing that same person draw a weapon and take a swing at them. So don't let the game mechanics color the reactions of the NPCs.
How about
not throwing a hissy fit and insulting all the guards you are trying to get past, or just taking the refugees to where the city they are trying to get into sent
its noncombatants? Seeing as Az005 both had an NPC officer try to mediate the arguement between the guards and the party, and also mentioned where the cities noncoms went, both seem pretty obvious.
Alot of people here seem to be completely missing the fact that the whole problem here was brought on by the players actions, and that the DM only tried to put on the brakes when the players started acting nuts.
This 'paladin/monk': insulted and threatened guards who said they were acting on orders, snuck into the city, mugged someone on the street, started a brawl with the guy they mugged in a cathedral, then ended up murdering said guy, in that cathedral.
The only problem I can really see here is that Az005 didnt point out the really really obvious solutions when it became obvious that the players missed them, and he didnt find out why the players were going so far off the deep end before it wrecked the game.
Before someone accuses me of railroading, my point here is that sometimes you have to be extremely explicit that it
is just a cow. DMs know what is going on, players dont. Sometimes they get stuck in a way of thinking and miss things that the
characters wouldnt. Getting agressive with town guards for no reason, especially when they are just doing their job, is out of character for a paladin. Az005 should have asked why the player was getting so upset. If it turned out that the whole party really didnt care for the noncombatant side, then he should have glossed that over, instead of letting bored players wreck the game.