No one can "claim" a name, as you say. You should definitely be able to use the name.
At the same time, it is clear that you knew that was her favorite name, and that she may name a potential daughter Emily some day. I don't believe that means you shouldn't use it, but since she had a strange reaction, I would approach her (taking the high ground) and have a conversation about this NOW.
She sounds like a very important, long-time friend to you. You should be able to have a deep/difficult conversation about this and make sure that it doesn't haunt the relationship, if indeed, she is having a hard time with it. Better to talk now than to wait than have her be (unecessarily) mad for years on end...