If a good friend I might try some thinly veiled criticism/comment like: "Oh that's interesting. I've seen so many people adding y's to names to try to make it unique" hoping she'd pick up on the "try" and recognize that it's still Emilia.
Or if she's a really good friend you could just be honest. I can really only think of maybe 2 people I could do that to though.
Oh, I just realized that you said her husband wanted it. You could say something like "Oh, I totally agree with you, Emilia is much better!" Even if she then says "Oh, but I didn't say I preferred it" the awkward thing would be more on her end for backing a ridiculous spelling.
Yes, I have hypothetical conversations in my head all the time.