For what it’s worth, I’ve met two (or maybe three) little Hermiones so they are out there, and people are using it. It was in the UK Top 1000 too, from the 90s until it dropped off in 2022, so again, people have been using it.
For the Hermione I knew best, people did bring up the Harry Potter connection on first meeting her, and it did linger, with some people making ongoing references, but that wasn’t the case with everyone. And little Hermione clearly hadn’t read/watched the series because they went over her head 
So yes, I do think it can stand as an individual’s name but I do think Hermione Granger will be brought up. So, is that necessarily a bad thing?
The character is seen AS inspirational by many and her wasn’t created by the series; it has ties to mythology too. However, without going into the politics, I wouldn’t want people to think I was a Harry Potter / JKR fan, so yes, that would put me off using such a HP associated choice. Obviously, it’s up to you to decide if you mind people thinking your big fans
Some in a similar style:
Calliope
Hester
Coraline
Amaryllis
Persephone
Hestia
Cressida
Leonora
Acacia
Ianthe
Iolanthe
Hero
Hecate / Hekate / Hekati
Halcyon / Alcyone
Honora / Honoria / Honor
Leandra
Thessaly