I can't see how that could ever work with a starship. For one thing, you can't shut down the computers even for a split second, or everybody will die. If you do it in safe stages, it will take much longer than shown - plus, the program will be fighting you every step of the way.
For another, there shouldn't be such a thing as a clean boot disk - the invasive program was shown to be capable of penetrating physical
firewalls (it jumped through Data's hand into Data), so there would be no place aboard the ship that would be safe from the program's attack. Every device, from the humblest PADD to the most vital sections of the central computer, would be contaminated - and so would all of their backups, because the program would make no difference between "primary" and "backup", "important" and "unimportant" in its vicious attack.
Of course, the program wasn't necessarily malware; Picard speculated it was a benevolent contact program that just happened to be overenthusiastic about its job. But that is even worse, as the program wouldn't behave like a predictable destructive intruder, only attacking tactically viable targets etc. Rather, it would rampage through the ship until it had shaken hands with the last cabin-vacuuming robot and fire-extinguishing subroutine...