I am afraid there is nothing you can do if these bitcoins are stolen. However you really are one of the worse companies available if you keep 100 bitcoins not in a hardware wallet, let me tell you that. Any other wallet can be hacked, the hardware one is so far un hacked. Never heard a story of one of these wallets being hacked. I am sorry for your loss but from the moment now you should start a new, forget those coins and the first thing your company needs to do is to buy a hardware wallet and use it for every transactions they will make.
From personal experience I am using the cheapest one Ledger HW.1 hardware wallet and every thing is running pretty smoothly so I highly recommend you and your company a hardware wallet.