Amazon is a mixed bag. For example, you don't sign your own app for the Amazon app store. This messes up data sharing if your customer bought apps from different stores, and it enables Amazon to add potentially intrusive code into the APK. Also, "associate" incentives are a big part of Amazon's marketing. I don't think they would view the Canonical deal as being bad for their image.
I like to think of Amazon as a brand I can trust. Having crapware sponsored by Amazon on my OS hurts that trust.