For mine, it's not Goon Swarm as a group that would concern me (the mechanics are such that it should not be possible for a group to actually control systems or regions). What I'd be more concerned about is any mentality or attitude bent towards exerting that kind of control to the exclusion of other players - because it speaks volumes about the type of players such people are. And a group like Goon Swarm don't have a monopoly on those sorts of attitudes - I would hate to see a prevailing attitude of domination-style gameplay creep into Elite Dangerous as it, imo, goes against what the game should stand for. Whether it is Goon Swarm or some group is irrelevant to me - nipping that sort of playstyle in the bud though IS relevant to me regardless of the perpetrator(s).
So when Frontier inject a story in to the game calling on players to help blockade a system you're going to say that Frontier have got it wrong and are encouraging griefers?