I think you can change it to Emmeline-Grace but I still think she’ll still primarily get Millie, Mille Grace and then names like Millie G, Emmy G or Eggy (last from teen friends & only in a nicknaming / gentle teasing culture like UK and Oz.)
Have you thought about changing her name to “Millie-Grace”? You’d still get a lot of people just using Millie & possibly Meg or Maisie - but I also think you’d get more usage of Grace with Millie-Grace then Emmeline-Grace.(I recognise you don’t love Millie but just to say it’s more likely to get Grace used.)
But if / given it’s essentially about prioritising the two names because you love them equally, and getting them more likely used together by more people, you could and should go for Emmeline-Grace. It’s a beautiful name and it’s about naming her the name or a name that feels and fits perfectly. 
If you’re ok for Grace to be used just by family and close family friends, then keep Emmeline.