Or some other way to deliver ads with copy and images, but through the backend. (that way the website author has complete power on what an ad actually can do on their website)
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.
The problem with affiliate marketing is that you must trust the advertiser in reporting conversions and paying. You can trust Amazon and some other businesses that way, but not a small business.
In most affiliate marketing programs the advertiser doesn't report the conversions - tracking and payment is handled by the affiliate network as an intermediary, which has it's own pros and cons. But they will fight for affiliates when commissions are due.
DM me if you'd like to talk more about that, I work in the industry.
Fallback URLs, location (for local businesses) and other customization options could be used to make it work better.
Some _optional_ Javascript could also enhance this, but not change it fundamentally.
Would it be possible to still have a syndicated ad network, but that it would feed you articles in some structured format, that you would get on your backend, and then insert as articles into your blog/website? This way you could format them any way you want.
Of course the payment model would have to shift from displays to something like overall performance of the ads (by scanning outbound clicks and associating them with purchases) and pay by month. And some policing in order to avoid stuff like getting the ad from the network and never actually displaying it.