EMDs by themselves? It would be ridiculous to drop an otherwise healthy site because of them. (It's also NOT what I see at all - almost every site I deal with has an EMD)
Google has set a higher standard for affiliate pages for quite a while now. Because for one thing, there's so many of them, and so many are poor quality. Even the ones that are acceptable quality are a dime a dozen (think of it - any lucrative affiliate program is going to have hundreds or thousands of participants)
So if you're going to rank an affiliate site, it has to be noticeably BETTER than average on first glance. It has to look like a site that happens to have a few affiliate links, and not a collection of affiliate links that happen to have a site.