So the FBI would have a lot of time before they had to worry about the consequences of a negative ruling, and they could drop the matter well before any precedent was set. Apple is in a trickier situation, in that once they've done the work, it becomes more likely that they'll face additional demands in other courts, or--and this is the worst case scenario--a few boneheaded legislators try to pass legislation on this issue. They've got a lot less room to work in, so if they could make this go away in front of a district magistrate without ever having to worry about setting any precedent (even if in their favor), they probably would.
0. http://www.law.georgetown.edu/academics/academic-programs/le...
1. http://faculty.law.lsu.edu/toddbruno/mandatory_v__persuasive...
But if there's an alternative method that's been proposed and the FBI is aware of it, the FBI can't claim that forcing Apple to act is the government's last resort. So that's the most likely reason they've halted proceedings and not any fear that they may lose.