Your question—particularly the more detailed statements and questions in your further explanation—are quite loaded. I don’t mean that as any kind of slur, it’s just that there is a ton going on in this area, so answering your question in full is going to be difficult.

Ok, we’ll start with the Catholic Church’s opposition to communism. I have covered that in brief elsewhere but I will try to summarize my argument. The Church’s objection to communism is that it is materialistic, so that if you did achieve the goals of communism you would have ignored the spiritual dimension that is so important to Catholicism. Social justice was important, but not as important as eternal salvation. This view goes back to 1891’s Rerum Novarum (at minimum) and was most clearly stated in Divini Redemptoris in 1937.

Now, as you state this might seem to advocate military intervention. There was a call for a crusade in Divini Redemptoris, but it was to be a crusade of prayer particularly undertaken by the contemplative orders. So while the Catholic Church was anti-communist it was not blindly so. As you guessed, the concept of a Just War comes into play. There was certainly a question of the likelihood of success—a requirement for the Catholic concept of a Just War. There is also the question of not doing more damage in the war than would be caused by the thing you’re trying to stop—another open question regarding Vietnam.

Moving on to the Berrigan Brothers, which is another loaded topic. Daniel remains a priest, but Philip married an ex-nun and I am pretty certain he was defrocked (though I can’t find my sources on him at the moment…the paper I wrote on Catholicism and Vietnam was written more than a decade ago…). Suffice it to say that while the Berrigan brothers were influential and vocal, they were fringe rather than mainstream. There was no consistent top-down Catholic opposition to the war in Vietnam that I am aware of, though there were some objections raised by various bishops as to how the war was being conducted. The Vatican has long objected to civilian casualties in war, especially those caused by indiscriminate use of force (and perhaps most notably in the arena of aerial bombardment). I don’t have any numbers on participation, but there were a fair number of Catholics opposed to the Vietnam War and a number in support of it (just like the rest of the US). Opposing communism, affirming your own patriotism, and politics certainly allowed Catholics to support the war.

There is one protest by a Catholic that (to me) stands out. Roger LaPorte was a member of the Catholic Worker Movement, had studied for a time as a seminarian, and was a sincere opponent of the Vietnam War. On November 9, 1965, he doused himself in gasoline and immolated himself in front of the United Nations in New York. The fires were soon put out and he was taken to a hospital where—amazingly—he was conscious. He claimed that this was “a religious action.” However, he did receive last rights including confession, in which he expressed remorse for his action. It was later revealed that he had not told anyone of his decision to undertake this particular protest action. Those closest to him in the Catholic Worker Movement asserted that they would have attempted to discourage him from doing so. This article from the day after his action tells the same story. Sadly, he was too badly burned to survive, and he died the same day of his self-immolation.

On the other end of the scale, many Catholics served in government during the war. There were also many Catholics in the military (either voluntarily or as draftees) during Vietnam. Overall, I would have to assert that there was no one Catholic position on the Vietnam War and the participation of the United States in that war. There was clearly opposition to killing innocents, to the indiscriminate use of artillery and bombers, and some opposition to the war on legal grounds. However, there was also a good deal of Catholic support for the government and the military as well. After all, we are dealing with a fairly long time period, a huge number of people, and a complex topic as well. I think finding a lot of variance in the reaction among Catholics to the Vietnam War isn’t surprising.