I've talked about our issues with hijinks and ruffian morale before, but I think I've hit a simpler solution which makes ruffians more perilous to employ, but does so without adding an additional roll to the hijink mechanism. Should a ruffian roll a natural 2 on a hijink attempt, he defects and betrays the guild in some fashion. If he's also caught on such a roll, he may betray the guild to the authorities in exchange for a reduced sentence, or he might become a mole. If he isn't caught, he may instead become conspiratorial and begin plotting against the guild's leaders, or he may sell the guild out to a rival criminal organization. Further, ruffians of 5th level or higher may defect on a natural 20, taking the big score and deciding to go freelance (this is also likely outcome should a remarkably-skilled ruffian succeed on a hijink with a natural 2). Such high-level ruffians may induce others to defect as well, at the judge's discretion.
So - a ruffian defection mechanic that I'll remember to use, and which generates minimal extra paperwork. As an aside, I kind of like a further proposed rule, that in certain high-law areas, should a henchman or PC thief roll a natural 2 on a hijink, even if they are not caught, they are witnessed. Wanted posters, going to ground, and other shenanigans ensue. This rule seems punitive enough that I would not want to employ it except as a means of characterizing certain settlements as being particularly law-abiding, though.