Thanks everyone.
Logoaway was just what I was looking for.
The preview function for that plug-in was a godsend.
In the end, I just used Virtualdub with the Logoaway filter, saved to lossless AVI and did the cropping, scaling and encoding in TMPEG (Lanczos algorithm).
The DC of Cyborg actually looks pretty decent now. At least the aspect ratio is correct, and the blur effect is far less distracting than the counters IMO.