Whilst I do love Elora, I would stick with your original choice. You picked Eleanor for a reason, you call her Ellie anyway and will no doubt continue to do so, so I don't see the point in causing her future hassles by changing her birth certificate.
Eleanor isn't that popular. It's not like you chose a top 10 name. Ellie no doubt feels really popular, as although the popularity of Ellie as a given name has decreased dramatically in recent years, many of the top 100 names can shorten to Ellie. I assume that many are still using this but opting to use a longer version on the birth certificate, like yourselves, which is why it appears to be sliding down the charts but is, in reality, still widely used.
My suggestion, if you want something slightly less popular, is to actually start calling her Eleanor rather than Ellie! If it really matters that is? If Ellie feels right for her, stick with it as who honestly cares how many other Ellies might be out there? She's the only one who matters to you.
If you're still going to call her Ellie, what does it matter which longer version is actually on her birth certificate? You really may as well stick with your original choice. Although I do like the suggestion of tweaking her nickname to Nell/Nellie instead. Nicknames can evolve over time, regardless of what is on the birth certificate.