Aside from hindsight being 20/20, the incremental impact of the war to U.S., lasting a year or so longer than perhaps it should have, was not that great. The US was winding down its efforts in the last few years. It would've been bad policy to just walk away and capitulate; the North Vietnamese took advtg of the opposition to the war to hold out.
In any event, your statement implies "the end justifies the means". That is dangerous, because a great many anti-social activities could be justified on those terms. The actions of southern segregationists in the past and anti-abortion clinic blockaders of today, to give some examples.
I suppose there was some of that, but the majority of what went on at least started as civil disobedience modeled after that evil radical Gandhi.
"Civil disobediance" is criminal activity. It is a violation of the rights of others. It is NOT protected free speech. Nixon was under considerable pressure by people in the country to stop violations of their rights -- people wanted to go about their daily business without suffering disruptions by illegal protest sit-ins in the streets or at colleges. The end intent of those "protests" was indeed disruption of commerce and education. Nixon had a duty to put a stop to it.
As to Gandhi, I'm not sure exactly what he accomplished, but there was terrible bloodshed when India and Pakistan gained independence. Doesn't sound like much of a record of success.
We know now that protesters were deliberately and specially trained to provacate in such a way to draw a reaction. The protest leaders were a safe distance away while their pawns did their dirty work.
Take a look at "The Ungovernable City/Lindsay" which talks about the intentional abuses against the police by the rioters at Columbia University.
That, and against whom he used those powers. Remember some of the legitimate critics who were under surveillance, and that the Watergate burglary and cover-up were targeted at the loyal opposition.
Those who released secret documents were not "loyal". In the case of Vietnam, it gave aid to the enemy since they therefore knew the US had no resolve to keep the war going; they had no motivation to make peace.
This was not about peaceful innocent protesters, but, as mentioned above, those out to disrupt the country.
I won't contest that J. Edgar was out of control, but he served at the pleasure of the president. Of course, he probably had the goods on Nixon as well as everyone else who could touch him.
Hoover was a powerful spin doctor in his day and he created a powerful myth about him. Nixon tried very hard to squeeze him out, but Hoover would not retire. If Nixon fired him, there'd be a huge outcry.