@Lee
1) Only a fool pays per impression for ads on websites. They are even easier to fake than per click ads. Only a bigger fool would sell ads based on what an advertiser tells him the response rate is based on his sales. So even though per click sucks, it's the best of bad options.
2) Most punters can't be bothered with AdBlock and NoScript, so Javascript just works for most advertisers. On the other hand, most punters do have AV software, which helpfully deletes cookies as an invasion of privacy. So cookies suck for tracking, even the good ones. Which moves you into areas on non-cookie cookies, which to my way of thinking are even more suspicious.
Yes, you'll want to do your own internal sales tracking on your own website. That will let you work with vendors who are better for you. But never make the mistake of thinking any of your payment options are good, because they all suck.