As I see it, the rewards program will probably be a positive thing for us. The rewards don't end up being huge, and Amazon is probably confident that the increased sales volume will more than make up for it.
Anything that incentivizes ebook sales (and book sales in general), will be to our benefit, even if only slightly. In particular, this is true of bonuses ("Spend $10 on Kindle books between Oct 31 and Nov 9 and earn 300 bonus points. Activation required.") Normally, you'd have to spend $60 to get those 300 points, so it looks like a deal, which means people close to ten bucks might be tempted to fill out that number with a less expensive (and probably indie) ebook.
Of course, the program is designed to encourage people to buy ebooks, since the bonus is bigger than it is on paper books. That's probably slightly to our advantage as well.