It isn't entirely clear to me what it is you're asking...
I *think* you're asking for an AppleScript wrapper that will launch an ffmpeg task to convert the file(s). That's pretty straightforward, but it won't make any difference to your initial concern over ffmpeg being 'very taxing'. ffmpeg, by its nature, will use as much CPU power as it can garner. Launching manually in Terminal.app, or via an AppleScript won't change that.
That said, if you want an AppleScript wrapper, something like this should get you started:
on opentheseFiles
repeat with eachFile in theseFiles
set sourceFile to POSIX path of eachFile
do shell script "ffmpeg -i " & quoted form of sourceFile & " -acodec aac -vcodec copy " & quoted form of POSIX path of sourceFile & ".conv"
end repeat
end open
The 'quoted form of...' syntax takes care of quoting the paths to make sure they're shell-safe (spaces, extended characters, etc.).
There are also several caveats here. For one there's no check that the files are actually valid audio/video files, although then ffmpeg would presumably fail gracefully. You could add checks if required.
Also, the script is set to run serially - transcode each document in turn. If you want them to run in parallel, a simple change is needed.
Additionally, large files may take a long time to transcode, so you run the risk of the command timing out. Again, a simple change here can take care of that if you run into this problem.