It opens some interesting questions about just what is our side and just who decides to be "on it." More importantly, I believe that the episode opens a fundamentally troublesome question: How often do we become the very thing that we oppose? And how easy is it to rationalize this behavior because - when we're doing it, it's "okay" because it's well motivated (read "it's us").
We seem to be living in a day and age where "having a good reason" stands paramount above an individually moral and/or ethical point of view. All one apparently needs is to feel slighted, marred, injured or overlooked to justify almost any behavior. It's not only possibly acceptable to pump shotgun rounds into your parents' heads, but, under the proper circumstances, it might be an act of political heroism.
We get to rail against racism and sexism with no regard as to whether or not, in our cause, we are exhibiting the very behavior that we speak to overthrow. In the midst of all this, a voice raised against the group-think will surely be considered a "troublemaker."
It opens seriously the question of "sides" at all. In The Prisoner, there was often a question of "is it us or them." In "Paradise" we open the question, "what's the difference."