I personally liked it. It felt to me a good way to lead into the Federation, where humans are no longer the xenophobic bastards we were before (atleast nowhere near as much). The xenophobia is not going to disappear especially after the Xindi attack and probably ramped up more with the delegations on Earth. Here are those aliens who attacked Earth, who attack our interplantary shipping, who come to Earth and steal our jerbs and romance our menfolk (poor Trip, dude was like the reverse Kirk when it came to alien women). Terra Prime existing makes sense and Terra Prime and the feelings that helped create it have to be overcome for humanity to move into the Federation era.
The final mission of the Enterprise going against the representations of humanity's dark side, its xenophobia and hatred, makes sense to me. And would help to explain why humanity was willing to embrace the stars rather then huddling behind our space walls, Terra Prime were some terrible people making babies to kill, attacking the moon (which we only got one of, be nice to keep it pristine), hijacking death rays, and menacing the Earth they claimed to put first. Admiral Robocop and his group was about the fear of the unknown, the fear of the alien and with their defeat and airing of their dirty laundry humanity was free to evolve into something new and better. Like space amphibians.