What ini are you looking at? The vanilla ini shouldn't have a launch animation specified.
The PTW/C3C ini clearly has a launch specified:
CAPTURE=AtlasLaunch.flc
I used this in-game and zipped up right from the game directory, so I doubt there would be any errors.
@AVY: I believe they burn up and nothing bad happens, most of the time

In any case, I think what happens to the boosters is the last thing SAC would have been worried about in case of nuclear war.
@Gogf: I check my PMs, I just have to sleep sometimes... maybe
you should check the amount of stuff in your inbox and delete some of it

POV-Ray can be found here:
http://www.povray.org/
As for other missiles, I will work on some, and I'm also open to requests.