I would suggest, as I have seen heavily used on forums, that you provide two urls for readers. One would be a direct link, and the secondary link contains the affiliate id. I personally like to think of it as along the same lines of a "contribute" paypal link on low traffic blogs.

I tend to manually remove affiliate URLs from links if I was not given a choice. I tend to be more favorable of signing up or purchasing with affiliate URLs when:

* I was given a decision to opt in

* I was notified that the link contained an affiliate code up front.