Did the NSA know who Mycroft was, know that he worked for MI-6? The way they said they knew about Diogenes and what goes on there, plus not helping Sherlock later made me wonder.
I feel bad for Joan, watching that man she tried to save get shot right in front of her. And then having those others gunned down right in front of her. I know they were all bad guys, but on top of being kidnapped that had to be quite traumatic. And then Mycroft is all "we have to talk, I have a lot to tell you..." (or whatever he said). I'd kick him to the curb. I, personally, don't hate him or anything, but that's a lot to process all at once and a huge secret he had.