Is it safe to remove a genital wart using over-the-counter freeze wart remover?

No. I believe if you look at the label that it is not indicated.
Yes. It should be safe if on the outside skin area of the genitals. Not to be used on the inside of the labia or vagina, however.
Drug facts label? Follow the package instructions. You might want to see your doctor to be on the safe side.