I was not referring to the procedure of tracking a click. I was referring the the procedure of bypassing the click process, which results in the same result you are complaining about - that publishers are not credited for delivering users to advertisers.
Unpreventable click fraud, among other things, makes CPC more vulnerable by advertisers who are concerned about it. The situation you described is an idealized best-case, which does not seem to occur enough that all advertisers are willing to overlook the worse cases.
FWIW, I think CPA has its set of problems. I am not a great fan of CPA. While there may be "more problems" with CPA, there is less infrastructure available to contain and control the amount of fraud that can be perpetrated via CPC, this making it more vulnerable than CPA.