Why? That's like saying that Amazon has a motivation to remove the Kindle app from iPhones and iPads so that you'll be forced to buy their Kindle. Amazon actually doesn't care if you buy their hardware or not, they only care about selling you content.
Don't get confused: Amazon will always sell you both razors and blades. They're not in the business of winning one specific category: they want to win everything.
That's why you can use the Kindle app on your iOS, or Android, or web browser. Or Amazon Prime on PS3/4, Xbox One/360, Roku, iOS.
They don't have to kill the iPad; they just have to win every book reader.