Well one way sponsors with multiple sites could help ward off the url rewritng is by generating unique linking codes, and run them all through one URL.
For example:
Old link
http://www.boysfirsttime.com/main.htm?id=biskoppen
Spyware just has to match "http://www.boysfirsttime.com/" in the url and rewrite with the authors affiliate code.
New link
http://www.nastydollars.com/JGG483gfeTGUE834754
Spyware author has no idea what site it goes to unless he visits each and every unique URL. Any rewriting done after the surfer visits the unique URL will be easy to catch.
What this would do is discourage the authors from doing simple affiliate code replacement since they have no idea which site to target, someone may even want to get together with a lot of sponsors and start a centralized linking repository, because the more sites you have listed the less inclined they would be to try. They could still hijack the traffic no doubt, but at least they couldn't easily target the same niche.