You can now change this setting either globally, or on a per-website basis in Safari Technology Preview 32: https://webkit.org/blog/7627/safari-technology-preview-32/

The options are: "Allow all Auto Play", "Stop Media with Sound" (the default), and "Never Auto Play".

Site authors following the best practices section in the WebKit.org blog should provide a play button for video-backed-gifs when "Never Auto Play" causes automatic playback to block.