In practice this won't stop all possible competitors, specifically those that flaunt patent law, but I don't think Amazon is one of those. Amazon could likely buy a license to the innovation from the patent holder for less than dealing with the courts would cost, in which case the patent system would be working as intended.
I run a little side-business, making a hardware gadget. My sales volume data is a sort of first-mover advantage. To compete with me, you have to risk guessing wrong about how many potential customers are out there.
This is what patents are supposed to be used for. You create a truly innovative idea and receive a patent for it. Then some large manufacturer, that has the scale to produce your product far more efficiently than you ever could individually, contacts you asking to license your idea. Together you work out a fair price for the rights, you get money for your invention, they get profit, you both leave happy, and the customer gets the best of both worlds.
But this really does burn developers of those original products who were originally brand partners.
I don't think Apple "owes" them anything, but I think they would help themselves by treating it as if they did. Especially where it's obvious that the OS-bundled app will win simply by virtue of being bundled. It's probably a legal issue where if they gave someone anything they'd open the door to being sued for a fortune, but it's horrible PR towards their developers.