I will soon be adjusting the mod to be assembler-based squad control, so one assembler per squad, and it will allow more direct control with the droid settings module (or similar) to control the specific things you want ONLY that assembler's squad to behave like.
If you are using the Unit Control mod you can do 'move' instead of 'attack move', which will do what you want. They will move away (fall back) instead of fighting. With my Robot Army squad selection tool, the move command is "attack move", I can't be bothered putting a non-attack-move command in there.