I may know why the builders and guards suddenly go all aggro, and it has nothing to do with a window. If you wait long enough, eventually Malachi gets killed by the elevator and they don't think it was because they elevator lacks safety features. I did a playthrough and Malachi was killed by the elevator but I had knocked out all the other roving builders that would have seen him. After I finished, I went in and set up on the table by the elevator that had a candlestick on it. Eventually old Malachi got chewed by the elevator and they all alerted. Sometimes other people get killed on the elevator at that point and sometimes it says I failed the don't kill anybody objective and sometimes it doesn't. Don't know if it'll happen every time. My first attempt either I didn't wait long enough or it may be some triggers need to happen. The second time
I still waited quite a while but Malachi eventually died on the elevator again. So if that isn't intentional, that may be what starts the issue.