Sorry for the late response, I am very busy at the time
I think it is possible to control the fleets with the Script Editor. You create two fleets, that belong to different races and you configure the races, that they treat each other as hostiles and you as a friend. Then it should work and you won't get locked - but it's much harder to control the ships then and it needs much scripting work
Too bad, that the sound effects aren't just files, that can be deleted
Another idea is to playback the sound effects from the soundfile, record them and insert them at time of video editing.