Wouldn't it just have to infect the vm like before and then reinsert the malware in the newly encoded video. No vm escape required a little meta thinking.
You could use 2 VHDs: One for the OS that's mounted R/O, and then one for the video file that's R/W. You only use the video VHD once, then destroy it. You also reboot between every file.
Edit: oh I see what you're saying. It'd be in the same encode. I'd have to think about it more, but I wonder if there's potential for playing games with the page table to mark things as read only or something. It's a fun thought exercise :)