Does anyone find it odd that Nick waits until after you've helped the Institute destroy the Brotherhood in the Commonwealth to get upset about the choice of doing so?
I mean, he's there the entire time (not in the Institute, but everywhere else - the fact he is always waiting for you when you relay out of the Institute is amazing, he's a good detective I suppose).
Thus he helps you kill Brotherhood, Railroad (yeah Nick, you helped me kill them all in cold blood and did not say a word...not even a loss of faction when I opened up on them), and whatever other collateral damage there was on the way to Institute domination (I stopped paying attention to who I killed after I turned).
And then, when you're done with all the killing and brought about a new status quo and stability (of a sort), THEN he gets mad at you.
Now, oddly enough, none of that hurts your standing with him (at all, I finished his companion quest after the main quest and he now idolizes me).
Point being, there is room for improvement on the companion faction dynamics.