To hide links from Google:
2.) Disallow that subdirectory in robots.txt, to tell Google not to look in it.
3.) For each link to Amazon, instead of linking directly, create a .php file in that subdirectory you made that redirects to the Amazon page. Then link to that .php file instead of directly to Amazon.
The result is that Google sees that you're linking to your own site, not to Amazon. But since the files are in a directory excluded by robots.txt, it doesn't actually read the files, and thus doesn't discover the affiliate links.