In which case, wouldn't that also make Dr. Soran a threat to Q? Shit, they really dropped the ball by not playing up on that to make him the most badass Trek villain possible. He can destroy stars, he killed Captain Kirk, and the Enterprise D was destroyed because of him. Q is also scared shitless of him. Dr. Tolian Soran, Trek's Most Dangerous.
Except that the Q/Guinan reaction was so ambiguous that we can't make assumptions about just what it was that alarmed him. Maybe she wasn't an existential threat to him; maybe she just creeped him out in some way despite being harmless to him, like the way I'm creeped out by ants on my kitchen floor or spiders in the window. Or maybe she just knew something about him that he'd be embarrassed by if it got out.
In any case, by the time they made Generations, they'd clearly abandoned whatever initial ideas there were about Guinan intimidating Q. They didn't "drop the ball," they just changed their minds about a rough-draft idea that they decided it was better not to follow up on. The same as numerous other abortive ideas in Trek history, like "half-Vulcanians" being recognizable on sight (implying that full Vulcanians looked more alien), holodecks being a novelty as of 2364, Trill being unable to go through transporters, or B'Elanna having a crush on Chakotay.