The company should appeal if the notice is addressed to them. This puts you in an even clearer position as the company clearly cannot have been driving.
If using b789's template you'll need to change any first person 'I' references to 'we'/'the company'.
As the keeper is a company, I'd be minded to beef up the point about them assuming the keeper is the driver... you could add in something like:
As we, the registered keeper, are a company, you clearly cannot pursue us under an assumption that the registered keeper was the driver, as this would be impossible. You can only pursue us as the registered keeper of the vehicle. However, as you have failed to deliver a Notice to Keeper within the relevant period prescribed by PoFA, you are unable to recover any unpaid charges from us.