I don’t get what homosexuality has to do with it. Daniel or Phillip Berrigan, the referenced priest(s), has to do with anti-war politics and stuff like that, aren’t gay, or weren’t even talking about it then. And they weren’t from Boston.
The song is about Julio and his friend doing something they enjoyed together. If Simon said this has something to do with anti-war politics, he flat out lied. Rock stars lie about their song lyrics a LOT, like when Blue Oyster Cult insisted that Don’t Fear the Reaper wasn’t about suicide.