Amazon is really hands-off with acquisitions for the most part such as Zappos and Audible. They primarily add to the offerings by cheaper fulfillment or server/bandwidth/cpu costs and more. I think they will treat twitch better than if it was just integrated into youtube.
Also, it shows a dedication to game developers and supporting marketing of games on their platforms and others. Amazon buying them is actually better for Twitch and the gaming/let's play type new marketing channels.