There is a prog somewhere that will remove them, But I've never used it.
I generally toggle my icons off regardless of server settings, unless I start hearing people calling me out, on my 6 and what have ya, so I toggle them on only to aid in the teamwork aspect of the mission.
What program and filter did you use for your movie.
I think its perfect for guncam stuff.
Ok I found it, but from what I just read it only works on the .trk format, not the .ntrk
But hey give it a try.
http://www.whtboys.org/IL-2/Utilities/Utilities.asp