As another former Amazonian (but not near payments stuff by any means), judging from the outside, this doesn't sound like it equates to the death of Amazon Payments at all.
The PR statements are very carefully worded to say, strategic partner that will be "processing a significant portion of Amazon’s total payments volume." If significant portion was going to mean anywhere near 100%, I'm sure Stripe would have shouted that fact from the rooftops even louder (what a huge win that would be!).
For my money, this really just reads like mostly a quid-pro-quo deal, you give me X% of payments volume, I'll give you Y level of commitment to AWS. With no insider knowledge of any kind, I would wildly speculate that "significant portion" could mean a value of X as low as 5-10%.