I disagree and think that increasing the cost of applying would indeed help this problem. If the number of applications is too high for humans to possibly review, what other possible solution could there be?
Start accepting CVs over snail mail. Much more difficult to automate, there is a cost already embedded in the process (72¢ for a stamp) and any attempts to automate this will be obvious.
The problem posed by this article is that companies are wasting candidates' time by making applying take time while offering no actual position.
What if we imagined that companies charged a fee to apply instead of charging candidate time? Then these ghost positions would be obviously considered fraud. We don't normally pay applicants for their time, but isn't a ghost position requiring substantial time to apply also a fraud on the applicant?
All I'm saying is, by removing the payment in time, you remove the fraud.
Applicant spam is an orthogonal problem that has other solutions. Linked-in could limit applicants to one application every 30 minutes, max 16 per day. Employers can use keyword filtering as they already do.