In this case the author says he created the link independently, because he thought it would be useful to his users. That's, by definition, a genuine, organic link.
I wonder if a link flagged by the disavow tool and confirmed by the user weaken the Google juice of the source site.
@MattCutts (or another Googler), is it the case?
We haven't been using disavowed links as a reason not to trust a source site. So it wouldn't weaken the Google juice of the author's/source site if the company that sent the email had just disavowed the link.
Genuine organic links can still be spammy. The OP seems to be a genuine affiliate marketer/spammer, it's not inconceivable that his links aren't treated with a ton of respect.
Some entities might try to say it is six of one & a half dozen of the other, http://www.seobook.com/brand-vs-affiliate-vs-spam but those same entities do not view their own affiliate marketing efforts as spam, even when they are pure spam http://www.seobook.com/google-lends-a-helping-hand
Look at the cloaked affiliate YouTube links to iTunes on music videos. And Google has invested in Viglink, RetailMeNot, etc.
In addition to those types of investments, it was Google's ad programs which funded entities like Mahalo & eHow.
There are zero affiliates which have made as much off affiliate marketing as Google has.