I thought it was perfectly clear - I refused the quest from the crucible knight because he downright said - this'll make you unpopular with the 2 other factions.. The dozen said the same when I took their quest.
FWIW: when I read "this will make you unpopular," the only "clear" assumption I could make, not having been spoiled, was that you will lose reputation with the other factions. "Lose reputation" does not lead logically to "you are declaring irrevocable loyalty to one side and declaring the others effective enemies now and forever" -- especially since the game allows you to have good rep with many of the factions at once. I wasn't aware till this thread (this is what I get for reading spoilers) that you would necessarily have to rely on one faction or another to advance in the game--the presence of factions in a game don't always indicate absolute sides you have to take, just potential enemies, allies, or in between. I've been playing through with a "well, I'll take the consequences of my decisions as they come" attitude so the revelation that I've apparently "sided" with the Dozens for doing a couple fetch quests for them (even though in other quests I've also killed them or worked against them) isn't rage inducing, though I get why the OP's annoyed. I think at least part of the issue is these quest do not feel like world-shattering decision making quests, but rather come off as simple fetch quest jobs you can be doing solely for the monetary gain of it without caring about the organizations' ethics or goals.
Looks like there is supposed to be another way around though, and hopefully all the OP will do is have to wait for the next patch---or accept that he can't quite do what he wants in this playthrough and see things through--who knows, it might still get interesting!--and then try what he wanted in a new playthrough later.
Perhaps they should consider how reputation plays in with "siding" with different faction, or not, and making that clearer. I actually got the conversation with the Crucible Knights where Clyver says, "Well, I can't ask you for your help, you're too friendly with the Dozens," but I assumed that WAS due to the fact I had a positive reputation with the Dozens, not because I had accepted--but not yet completed--a certain quest (because how would he know that I had?).
On the smaller matter of "but you kill a patrol" -- IIRC you are attacked by them without provocation, so you can defend your actions later--and I believe your reputation does not suffer. There are other places where you are attacked by Dozens or Doemenel likewise and it doesn't necessarily hurt your rep. Maybe it should? IDK, but defending yourself from an attack you didn't incite isn't a declaration of war against a whole side.
Edited by DeathQuaker, 07 April 2015 - 06:18 AM.