That being said, I think I will take it off of the site because it can be scary if you don't look at the code. Thanks for the suggestion!
At the end of the day, it wasn't worth spending the initial effort to build against that. I intend on doing this in the future, but for now I'm willing to accept the risk of having an incorrect redirect count and get it out to more people in the meantime.
To OP, in the words of Hank Williams "I've been down that road before..."
I wrote a FF extension for our site that did something (I'm guessing similar), look at the site, and do the appropriate redirect with some ids and what not so i could track the charity for CJ/LinkShare/Amazon/whatever flavor. Theicon would turn green if you were affiliate shopping and I was taking redirects from Slickdeals and sites like it and making them my own transparently. You may have a newer, better method that gets around agreements sites make but from my experience, the affiliate houses (and retailers) much prefer actual driven traffic to a scraper like mine (and maybe yours). In retrospect, I can see that it was essentially a leach. I wasn't really encouraging many people to do shopping they otherwise wouldn't have done (well that would be the retailers point I guess). If I had any influence it was only marginal and I was taking revenue directly from direct traffic sites which, most likely, weren't happy and might not continue to drive traffic to certain retailers if commissions went down by a noticeable margin (or link jacking was allowed in the TOS).
I haven't read your code, I'm purely guessing as to what it does, so if I'm offbase let me know and I'd be very interested in your approach).
EDIT: After finishing that novel, I actually looked at the site. Does it just redirect any link to Amazon? I was expecting some link-jacking and ID insertion, so maybe nevermind. Mine was charity based as well (similar to Goodshop) but a bit more aggressive (in the charity's favor) which is where I believe the downfall to be.
Shouldn't it only need to access amazon.com? E.g. once it detects my browser is on amazon.com, just redirect to smile.amazon.com. What else does it need to do?
But, as someone who's looked into the legality of this (I was building something very similar, but with a narrower charity set than the OP's), it is against their terms of service.
This chrome extension is really cool, and good for just forgetting to use charity affiliate links, but if your charity has an affiliate account that's the best way to do it right?
I used the eBook link to amazon.com on this page: http://37signals.com/remote/
For some reason, it seems to be working fine for me.
Amazon isn't just giving out free money. Affiliates are meant to drive traffic to the Amazon website. This service doesn't seem to do that.