That's a great question, and one I've thought over at great length myself. The only answer I have for you is that it is in my best intrest to keep them as a client too. I'm open to all suggestions. If you have a suggestion for some sort of traffic metric to pay affiliates for, please share it.
Shak mentioned above co-branding and providing materials to affiliates so they can essentially market the product themselves. So I suppose the answer to your question could (if this direction is taken) be "Yes, you can sell the software.". I don't know if that is the best solution, though.
Again, I'm trying to create the perfect program, so it benefits everyone concerned. Please keep shooting holes in this. I've learned a great deal already. :)