It's fair enough to mention, "if you engage that frigate you will incur an Imperial Bounty, a 10 point obligation for each of you since they know all of your names already. Do you proceed?"
It's perfectly okay to fudge the rules a little if it suits the story.
Do they get a benefit for taking on that Obligation? For example, do they get a cash handout from the Rebellion for engaging that Imperial frigate? If there is not a benefit, then there isn't Obligation. There will certainly be consequences to the act of attacking the frigate - including reprisals - but that's not tied to Obligation, and fudging the Obligation rules like you suggest is screwing the player as much as mishandling XP or credits.*
* To which I mean, you don't tell a player that he prepares for a mission and spends 20XP doing so - without having that XP actually do something (skills, talents, etc.). You also don't tell a PC that walking into a weapon shop just cost him 5,000 credits - unless he walks away with something of value.