It seems kind of paranoid to suggest that Amazon would manipulate an API that's so central to their business for the purpose of forcing an minor acquisition. Not to mention it would probably be cheaper to just buy the target for a few million dollars.
They cut off data access, right? That sounds exactly what has happened multiple times with other companies to drive an acquisition. I bring up Zappos because Amazon forced a sale there. All they needed to do was threaten a "diapers.com" where they forced an acquisition in that case by (unsustainably) undercutting prices. Companies manipulate their platforms constantly to achieve their business goals.
Goodreads is not Zappos. They are at least an order of magnitude apart in size, if not two, and Amazon is larger now too.
Making large strategic plays makes sense when you're talking about a purchase that is a large percentage of your own company's market value. It does not make sense for a tiny buy. This would be like refinancing your mortgage to buy a Big Mac.