I don't know how uncommon you are comfortable with, but for me Indigo is about as uncommon as it gets. Never heard of it as a name. However it is very familiar as a word and unlikely to get misspelled or mispronounced.
I’m not sure what “too uncommon” means to you. It’s a word you are using as a name, which is done a lot in general, but I’ve never heard of indigo as a name. My daughter goes to school with an Indie. Not my style, but I think it’s fine.
Re: Indigo (Indie for short) for a girl?