The config file has different lines for different types of videos so you can selectively enable/disable them. If you do as shown below, it will leave the intro videos and any scripted videos intact but only disable the ones for assassins and spies.
Code:
[video]
movies = 1 ;game launch video, faction intro movies
event_movies = 1 ;historic_event fmv, I think also the victory/defeat videos, may also include princess marriage
assassination_movies = 0 ;assassination
sabotage_movies = 0 ;sabotage
infiltration_movies = 0 ;spy infiltration
There is also the event_cutscenes option under [game], I'm not sure what that one does. Users of your mod won't be able to re-enable these videos without editing their config file which is akin to editing any other file in the mod (i.e. nothing you can do about it so it's just as good as another fix).
The other option is to edit descr_movies.xml and basically delete all the contents. This file links those assassination, sabotage, and infiltration events covered by the configs to fmv files. You can likewise change/remove the intro, victory, and some scripted movies in descr_movies_tracks.xml.