I've rescued the civilian fleet admiral and Admiral Raan mentioned that it'd be super good to destroy the Reaper base ASAP, but she also mentioned that the Quarian civilians will snuff it if I don't take out the Geth fighters. Is this false jeopardy, or do I have to make a real choice here? If I do, what are its ramifications?
No, it is in fact required for a peaceful solution to the Geth/Quarian conflict. If you do not complete this mission before taking out the Reaper Base you will not be able to Charm/Intimate a ceasefire.