As A GM I've considered not rolling, but letting the numbers be a general guide. I don't like the idea of rolls + chart dictating what will happen. Sounds like a different sort of game to me. Instead I would look at the numbers to give me clues on whose obligation would kick in the most and try to balance things across my adventures to meet those percentages. Then I would have free reign to cause the bounty hunters to show up when I want to or some other obligation to kick in at the right time for more dramatic effect. Leaving it to a roll and chance is not my liking.
I'd suggest taking a listen to Sam Witwer's comments about Obligation in the most recent Order 66 podcast.
Having a PC's Obligation come up doesn't mean that it has to overtake the story you've got planned. It could just be that something comes up that reminds the PC of their Obligation in some fashion, which stresses them out and in turn causes the other PCs to feel a bit stressed out because their buddy is stressed out.
And if does play a more active role in the adventure, it doesn't have to be a major one. Case in point, during the Friday Skype game I'm in that Cyril runs, I had my PC's Obligation (the fact he's a wanted fugitive from the Empire for being a deserter) come up. It added some roleplaying opportunity and a very a brief skirmish, but otherwise didn't subtract from what the other players were doing. And in a prior session, another PC's Obligation came up, and had to deal with a bounty hunter over a game of sabacc while the rest of us were awaiting an attack on the hover train we were aboard. Said Obligation had minimal impact on the overall narrative.
Granted, rolling doubles probably should mean the Obligation can have a major effect, but I believe Cyril's got a good approach in the he makes the Obligation roll when he's designing the adventure, and incorporates any Obligations into the adventure instead of having it come up as a surprise at the start of the game.