Well, the notion that Minmay's singing made everyone all lovey-dovey, dreaming of butterflies and pretty flowers, and that they all just laid down their arms and said, hey, screw this, lets hold hands and sing koom-by-ya, is totally wrong. There is no magic involved with Minmay, this isn't Macross 7. For the Zentradi, Minmay was simply the face of human culture, and it worked. And then they beat the snot out of the ones who resisted.
SDF Macross did not have a "peaceful ending", the war stopped because the UNS and its Zentradi allies won by killing the rest.