Affiliates work fine for E-commerce and performance advertisers that can track conversions. They work considerably less well for cost-per-click advertisers and brand advertisers because the advertisers can't trust the publishers either; there are plenty of spammy publishers who will send fake clicks and impressions your way for $$.

This is the major reason ad networks put JS on publisher sites. You can't give a website author "complete power" any more than you can give an advertiser complete power.