The "simple" solution to this is diverse decoding-encoding. In two VMs you install two different implementations of a video transcoder. In one VM with one implementation, you decode the video, and in the other VM in a different implementation, you re-encode the decoded video.
To succeed, the vulnerability would have to work against two different software implementations of a decoder and an encoder, and predict which ones you'd use. For extra effect you could randomize what you use each time. Attacker would have to infect a whole lot of videos to finally hit on the one that you decode-encode in the right combination using an incredibly complex vulnerability.
Nobody in their right mind would ever develop this vuln, just like nobody in their right mind would implement this defense :-)