What's Pinterest going to do if this option doesn't exist, remove the links? No.. they could change the display algorithm to display links with their affiliate code more often, but that may mess with quality of content and click-rates..
Pinterest has every right to monetize their website in the least intrusive way possible. These referal links are transparent and provide a neat way to get some income.
What suprises me is how they are giving away 25% of their profits by using a third-party service instead of making something themselves.
Some (many?) programs will need to adjust their terms for this practice, or they may face one of those Groupon-like situations where a family bakery needs to serve 100k muffins, at a loss, in a weekend.
They assume a proportion of the buyers will be repeat purchasers. Paying for a loss-leader product for 100k casual visitors with unknown demographics or purchase patters is riskier than many businesses are comfortable with (for good reason!).
Also, if you are Fred's custom napkin business, and you usually sell 10 napkins a week and suddenly you receive 100k orders you are going to have a problem scaling a physical business that quickly.
Say if those 100,000 people came through an affiliate link, they only make $900,000.
If you're Amazon's affiliate manager, indeed your first thought is, "Wow, Pinterest is great! Look at all these sales"
But your second thought is, "Wow, if I just drop Pinterest from my program, I'll make an extra $100,000." In its current state, Pinterest will not do anything to stop these sales from being generated, so the merchants are just throwing away money.
The real problem here is that Pinterest doesn't deserve the commission, Pinterest's users do.
Also, I am not sure anyone "deserves" the commission. It isn't a right.