Some very quick observations:
1. The subject of the encounter (rules/regs governing extending the duty day), although interesting, does not bear on this at all;
2. Regardless of right or wrong on the rules, the verbal outbursts were unprofessional;
3. As soon as he touched you his behavior transitioned from "unprofessional" to "criminal."
There is simply nothing, short of self-defense or the physical defense of the aircraft/crew/pax/others that would justify one crew member grabbing another crew member by the throat. Although laws differ, nation to nation, and I cannot begin to speak intelligently to the laws of the jurisdiction in which this occurred, in the US the mere touch of the captain upon your throat would consistute battery. This guy is dangerous. If he tends to act out his agression, he's in the wrong line of work.
I know I sound like I'm giving legal advice here. Trust me, I am not. I've just provided my impressions, based upon the info you supplied. In short, my opinion is that the captain's behavior was just wrong.