After fiddling around a bit, I found a working solution:

1) Locate the games video folder. Should be something like \GOG Galaxy\Games\Battle Isle 3\SDI\DATA\AVI

2) There you find all the vids used inside the game. The important avis are :
api900.avi (almost empty placeholder avi!)

api980.avi (Intro)
api981.avi (intro2)
api982.avi (intro3)
api997.avi (outro)

instead of just deleating the movies, which would lead to error messages on end, we simply REPLACE any unwanted movies with the empty one.
example: rename the 980.api into 980.old or whatever you like.
Create a copy of the 900.avi and name it api980.avi and place it into the folder with the rest.

Do it accordingly for every video you want to get rid off.

That should lead to 0.5 seconds long intro/outro movies and no error message. :) have fun!