Just play the main questline with your default lethal weapons but make sure to:
-Don't let DI to knockout an enemy with her disruption weapon just to be safe.
-In the factory sublevel, after assembling the war bot, don't let DI change its ammunition to disruption rounds.
I did this by speedrunning the questline on tourist difficulty. You can't ally the ghost gang by doing this so you have to kill every member as well including Blue.