Automating existing work is more than just programming; a big part of it is expertise provided by people knowledgeable about the existing workflow. None of the projects I've been on that involved automating existing work involved only programmers and no one with experience doing the work.
If you go with a principal that if you are involved in automating the job away, you get some reward, the accountant may have some incentive to help (especially if it is likely to happen, but with perhaps lesser quality -- but still perhaps a net cost savings to the company -- anyway, which would result not only in the company getting less than if the accountant was actively involved, but the accountant getting less as well.)
No, I actually said the opposite.
If you get automated away, by yourself or by anyone else, you instantly get the bonus and you're instantly fired.
The accountant has every incentive to either be an amazing accountant so that any automation would be a pale imitation (everyone wins), or he can choose to automate himself away, move to the next job, automate himself away and pick up the bonus there, and so on (everyone gets their due).
This is competition, and I think it's a happy ending for meritocracy. The only people who lose are those who desire to continue to be paid while not generating value.
Of course this does mean a lot of people out of jobs, which is the crux of the article, but I don't think it's a fault or weak link in this employment model.
That's the kind of situation that needs to be handled.