I just finished playing a game where the quorum card "Assign Chief of Staff" was in play. This card reads "Keep this card in play. Before cards are added to a Skill check, this player may discard this card to make all Politics Cards in the Skill check count as positve strenth." My fellow revealed cylon player played the super crisis card "Bomb on Colonial One" in an attempt to reduce morale to 0. The humans then decided to use the "Assign Chief of Staff" quorum card so that yellow cards count positive for the skill check (normally just red, blue, purple counted positive).

At first I thought you couldn't do that, because of the rule that super crisis cards are immune to abilities that affect crisis cards or skill checks. However, the wording of the FAQ states that "Super Crisis Cards are treated like normal Crisis Cards, but are immunte to all character abilities that affect Crisis Cards or skill checks". That ruling makes it sound like you indeed can use quorum cards to affect Super Crisis cards, which seems to go against the spirit of the FAQ rule but not necessarily the letter of what is written.

Has anyone else had this come up in a game, and how do you all interpret the rules? Can anyone point me to an official ruling that this quorum card can indeed be used on super crisis cards?

As you say, the rule only prevents character abilities, so Assign Chief of Staff is fair game. Hope this helps!