I don't mind having 8472 agree to a truce because they weren't the aggressors in Scorpion, their savagery was an overreactive self defense.
But I hate the way they went about it. It made no sense for them to do the Soviet Americatown thing, there's no reason for Species 8472 to do that. They could have written an episode where Voyager had to somehow convince them they weren't like the Borg, that was more violent and less sentimental, and it could have been a great episode where they really had to apply Star Trek's original mission statement and find common ground with a completely alien species.
but that's exactly what the episode was! they were learning to be human so they could observe the AQ, they thought that humans were a threat. Janeway did have to sit down and convince Boothby that they weren't a threat at all