Hermione is lovely, and pretty well nickname-proof, which you can't say about
Winifred or
Minerva (which is more
Harry Potter than
Hermione, IMO).
There's the Shakespearian link as well, which you could introduce to balance the Hogwarts element.
I think
Hermione Thomasina works very well, and flows better than
Winifred Thomasina or, especially,
Minerva Thomasina.