By making him an agent of his company's customer service to remove a passenger who is in compliance with the law, regulations, and the company's own contract of carriage, and then use FAR 91.3(a) as an excuse to say the pilot must be obeyed is poor logic. And I am a pilot (and a former CFII). I think it makes flights less safe to inject the company's demands into the cockpit. They do not matter, what matters is safety. That's what his FAR is about, not to enable the pilot to be an ass to passengers on behalf of his moronic company.
And claiming otherwise damages the necessary trust that we're supposed to have, and should have, with pilots and crew. Their primary purpose is to save your life. It is not to pour sodas, or appease the company CEOs profit needs by being jerks to passengers, and throwing them off for business reasons.
As for the police, I think that was an illegal assault on the part of the officer, and given the available information the passenger wasn't breaking any laws, so the police being there was inappropriate in the first place, they shouldn't have intervened and should know that.
Edited a few times to remove foul language :-D
Too many places I frequent have had crews, and especially airline pilots, basically pulling the "my word is law, there is no appeal and no review and nobody above me but God and even He only has an advisory role" crap.
More recently, examples of pilots refusing to fly with Muslims on board. It's more of this "what I say goes" logic, and the gate agents were not able to tell the pilot to take the corn cob out, and take these passengers to their destination.
Passenger was not disrupting the flight in any way. Passenger was behaving properly and then was forced to leave for the convenience of the airlines at great inconvenience to himself, despite the fact that he was as entitled to remain on the flight as any other passenger -- as in this was unfair to him and him alone. It was also made clear to him that he was not responsible for being forced to leave as well as the fact that all the other passengers felt the exact same way as the passenger who was being forced to leave.
Those regulations do not trump the pilot's authority to directly order a passenger removed for disrupting a flight, even for trivial reasons. See this article that discusses various airlines' history of expelling passengers (warning: autoplaying video with sound), http://fortune.com/2016/05/11/airlines-kicked-off-passengers..., or the FAA regulation directly, https://www.gpo.gov/fdsys/pkg/CFR-2011-title14-vol2/pdf/CFR-...
Moreover, the police order may have been mistaken but that in no way absolves the individual from complying with said order. He should have resolved the issue with litigation afterwards.
(Again, to make my position clear, the airline behaved quite badly but so did the passenger.)