Well if you are up to it, I would meet with this dad and the mom and have a heart to heart. Better to just put it out there and let the chips fall where they may. If you need the school Counselor , Assistant Principal or Principal to mediate, do it. You and your daughter have nothing to worry about or be upset about, This is his problem.
Sometimes Adults misbehave, explain this to your daughter. Also explain his tone is what actually makes him scary, but that may just be is voice. I am trying to recall a children's book that has a character that is a gruff sounding and looking man in it, but you find out he is just "a worrier and a loud talker. "
I would remind the other parents , these are just children. That your daughter and their son are good friends and you can tell that they like and respect each other.
Then you tell them, that IF they cannot treat your daughter with respect, without making her upset and nervous, then you are no longer going to be able to allow your daughter to play wit this boy. And next year you are going to make sure they are not in the same class room.
My father had a "Presence and a tone". We were mostly used to it, but no other children that we knew grew up like this, so it really made them feel uncomfortable and nervous.
My mother tried to explain this to him, but he always became defensive about it. He was acting like his own parents had treated him, he did not know any differently.
What ended up happening is that we just did not invite people over.. that is until our parents divorced.
This dad needs a wake up call. You cannot solve his problems, but you can put him on notice you will not accept this behavior towards your daughter, ever.
He owes her an apology, with you as a witness.
I feel sorry for his son, his father is a Bully Parent.