Whats the actual goal of the GM here? Of the players? Are both satisfied?
the GM has basically turned the the PCs from heroes to zeroes. By virtue of DM fiat.
the players may have just wanted to do some good in a world where they can, and the DM not only thwarted it, is discouraging it.
So, while it may be realistic to determine that bringing in numerous refugees, mass amounts of gold will impact a society in a potentially devastating way, it's not very fun. And quite possibly not the kind of game your players want to play.
Or it's called a story arc. At the end of the Dark Knight, Batman is assumed to have killed Harvey Dent and is a wanted man, but will still be trying to do good. If storyline is DM fiat and that upsets you, then you should probably just not play.
Personally I roleplay to see what will happen when my character is challenged and what he can do with my group of friends. Will everything teh DM ever throws my way be something I enjoy? Well no, but then it would probably be boring if he was just pandering to us all the time. Showing back up in a town where you thought you had a bunch of friends and instead ending up held captive as the ruiners of the town is certainly an exciting roleplaying opportunity in my book.
Do we try and talk our way out of the situation? Do we decide it's just easier (and possibly more humane) to kill them and go on our way? Do we run away and do what we can to dodge any potential rewards and assassins? Do we run and try to clear our good name? Those are some very interesting options and even if it wouldn't be a typical campaign, well who the heck wants typical?
