We had exactly the same dilemma. All through my pregnancy dd was going to be Emilia. Every single person I mentioned it to assumed I was saying Amelia (I asked them how they would spell the name and they always began "A...").
In the end, we decided we couldn't saddle dd with a lifetime of explaining "It's Emilia, with an E, not Amelia.."
Dd is called Phoebe, and it suits her perfectly 