I would say your second interpretation comes little bit closer than the first to the meaning of the original quote, but it's still not 100% accurate.
MacMillan dictionary says "an apt pupil" is "good at learning", so I would say she did "well", not necessarily "excellent".
Also, the extra analysis you give in your first sentence (about how her success was less impressive because she had lots of time to spend on the one subject) is not mentioned in the original quoted sentence.
Thirdly, the expression in your second interpretation, "she learned a little other things" isn't really idiomatic in English, so I'm not certain exactly what you mean by it. When the original sentence says, "she learned little else", it isn't telling us proudly that she learned some other extra things as well. The emphasis is on little. In other words "she learned almost nothing else."
So, including the beginning part of the quote in brackets, I think the meaning of that sentence is:
[Because Ellen and Mammy worked toward that goal, as Scarlett got older ...] she did well in this subject, but she did not learn very many other things.