to put on the faction armor, and take out the guards. The guards are the ones in the beefier armor, they can detect you behind your disguise. So, take them out one by one. It takes a long time, but after you clear them out you can make a savegame right outside the boss's office and then you can run in there and try to activate the dialogue before he goes aggro. After a few tries you will be able to do it. So then after you get the quests you just run out of the facility (he may follow you, but just ignore him and he will run back), then do the quest stuff, and then go back and do the same thing each time you have to talk to him.