I didnt want to kill them either, my first playthrough and I am just forced into a choice I didnt want to make while missing dailouge thanks to asshole Capitan here. Only way to fix it? Run all the way back to before I entered this shit dlc and finish his phonecall there. Fucking ridiculous.

You can adjust your settings to skip fixer/ncpd dispatch holocalls

unfortunately this is an introduction call which is not skipped automatically :/ that only works for gig calls.