Homeschooling kids who ace everything else often do less well on social studies because it is very subject specific. What I mean is that if you know everything there is to know about Native Americans but don't read enough about the Norse/Vikings, then you won't do well if they ask about the Norse. It's not as easy to glean the knowledge from just life as it is to get the math, science and LA stuff. We just don't see the Vikings every day like we do the other subjects!
I'd also recommend asking to overrule the decision. You can even offer to "catch her up" on the areas of social studies that she missed if you think that would help to persuade the powers-that-be. But it seems like they've set the bar unreasonably high, and it seems pretty clear that she's an excellent candidate for a skip.
