Been a while since i played, but you dont need to pay Victor at all, he will remove the virus when he gives you the kiroshi eyes and hand upgrade during the mission even if you dont have money (i think you might have to equip both of them at the cyberware screen when he does the operation, not sure about this part, its been a while)
You can pay him back later if you want to access his store, but thats not really needed since 2.0 has changed ripperdoc stock and you can get the upgrades from other doctors.