The pro version of Free Link Cloaker does this, but isnt ready for sale yet.

Create a framed page. In one frame load the discount page, and in the other load the affiliate link in an invisible frame.

This way it load the affiliate link to drop the cookie, and displays the discount page.

Not completely sure I understand the question, but it sounds like you might want to redirect the user to a different page?

If so, why not use a PHP redirect.