Have you tried simply setting the embed code wmode property to transparent or opaque? I cannot say if this still disables it but back when Stage3D first came out I had to do this a bit to get some content to work. wmode="transparent" or wmode="opaque" would disable hardware acceleration (fixed some h264 playback issues too). Might be worth a shot.
i've tried all possible wmode options, however they don't really affect the video playback problem I am facing. the only way to fix it is to disable hardware acceleration in flash settings.
to be frank, I find current situation quite irritating - every service providing video experience to the users via flash is having special page containing advices for HW acceleration disabling:
vimeo: Playback Issues on Vimeo
etc... millions of them
and the only way to disable hardware acceleration is to go to the flash settings and disable it manually.
I wonder if there is anyone from Adobe reading those topics? For the last two weeks I googled a lot this topic, people like me are trying to provide best user experience, but they can't. I found similar to this topic even on those forums. The author also had to go for the manual 'resolution' approach. Come on guys, this is 2014, there should be more smarter ways doing this like providing actionscript methods for changing this option.