I am actually all for a Gorn Empire as portrayed in SFCII, so long as the Federation didn't go all Starship Troopers genocidal on them and the Gorn fired the first shot.
Alternatively a civil war between the inevitable militants in the Federation that would pop up as a result of the SNAFU in this movie and the noble stalwarts of the Federation would be really cool and a way to inject moral ambiguity into the story while allowing the series and Federation itself to be as they should.
I originally thought Gorn for the sake of having something new and exciting. But the more I think about it, the more I worry they would look silly and cartoonish, and they wouldn't fit with the 'real' feeling of the Abramsverse.
I like the 'threat from within' idea, but I just dread the inevitable arguments about violating Roddenberry's vision - if I recall correctly a lot of people went nuts when the DS9 Homefront/Paradise Lost episodes went to air.
As long as the threat from within represents exactly the perversion of the Federation that I am talking about you won't hear any complaints on my end. I would love to see an on-screen treatment of the overly militaristic elements of the Federation getting a good drumming in the last act or so, especially if they overwhelm the Federation initially.