I think you should stick with Scout Eleanor. I'm a school librarian, and I see 500 children a week. The kids' official names are always on the class list, so if she is Eleanor Scout called Scout, she will have to explain it to every teacher each year. Like Abby said, kids have no sense of names being unusual these days. If a teacher mispronounces a name, the other kids will gleefully correct her, and act as if everyone knows the correct pronunciation. Don't worry too much about the adults. When I named my daughter Susannah, every adult sang Oh, Susannah and had a comment. None of the kids thought twice about it.
You love the name Scout, and now that you are a parent, people will judge *everything* you do. bottle or breast, organic food or not, too many activities or too few, whether you don't do enough or are too bossy at the PTA. Stake your claim now as being confident in your decisions by naming your daughter your first choice name.