Yes, ultimately it comes back to the registered keeper/owner. But...
I am not sure if it is still the case, but a few years ago someone challenged in the European court, that as speeding was a criminal offence, they had the right to remain silent. They won the case and that is why most speed cameras now face the direction of oncoming vehicles - for photographic evidence - when people refuse to answer who was driving.
I don't know if they have gotten around that now by automatically making the registered keeper/owner responsible. I don't see how they can. After all, if you were not driving, then you were not speeding - simple as that! Why should you take the points and a fine for something you didn't do?
I would continue to insist that it was the ex-employee that was driving at the time. Surely you have work records for that day and obviously you know where the offence took place? Try to match the two together. Hopefully it will get dropped in the end - or end up with the right person.