I really like
Matilda. It has an old-fashioned slightly off-beat feel.
Minerva is usable, and I appreciate the goddess of wisdom association and Prof. McGonagall. The nickname
Minnie sounds childish, and the "nerva" ending bears a semblance to nervous, so it isn't a favorite.
They wouldn't be confusing as sisters. They could work together, but they don't compliment each other either.