Well, the problem that Seri is facing here is pretty much frying pan and fire.
If he says "no, I'm not affiliated in any way with *insert x*, any attempts he makes to portray unsavory actions will be simply glossed over by die-hard proponents of the Fed-as-good-guys paradigm. In fact, it's likely that they'll claim that they are affiliated with some part of the Fed, and that the Fed officially condemns Seri. I've seen this happen before.
On the other hand, if Seri does claim even the most tenuous of connections, he is "god-moding" by some standards. But let's be honest - we all claim some connection to our faction of choice. Ghost Festival claimed to be a capsuleer experiment by the Dominations. Many Amarrian players - including many in PIE, claim to be Holders. Any time we try to create any connection between ourselves and the pre-written story, we engage in a bit of this by-fiat storytelling.
The difference between acceptable use of such and "god-moding" is one of degree. Ciarente created a planet and gave it its own culture and customs. Is it right to claim that since the Eve writers intended no such planet, Cia is "god-moding"? Hardly. Without some liberties being taken, there is no RP.
To say that Seriphyn couldn't find some agents somewhere willing to authorize his actions, in a Federation of trillions, seems odd. He's a capsuleer, insanely rich, and likely with some amount of influence. From an OOC perspective, it's a minor sin, certainly no more egregious than the claims Verone makes of actions taken against him by "lawful authorities", or Stitcher's claim that he was chased by the Provists, or the statements many of you pirates have in your bio's regarding CONCORDs files on you (after all, who are you to say what an NPC organization thinks of your characters, hmm?)
If Seri doesn't somehow tie his actions to a Federal NPC group, he will be quickly deprived of his "status" as a loyal Federation capsuleer by those unwilling to admit any faults in their own faction. So he, presumably without guile, came to reasonable conclusions as to what an NPC group might participate in, and made a story out of it. And it was interesting.
It's all very well and good to say that this isn't personal, but those statements ring rather hollow when you realize how often others do the same exact thing that Seri did, and are congratulated for their efforts. The reality is that somehow Seriphyn seems to get designated as an acceptable target because he irritates some people.
I'm not on a crusade for Seriphyn here. Frankly, my interest in this comes down to "well, that's not fair." And you who are criticizing Seriphyn, in the end, may be finding him at fault because he went two inches over your personal preference as to how one should use NPCs and background info.
Which, in the end, is "your RP is wrong".
And I understand, I really do, the desire to prevent someone from running over an NPC organization with fantastic changes to their nature - i.e., "the Theology Council has deposed Jamyl and crowned Vikarion Emperor!" or something similar. The difference is, again, one of degree. Seriphyn's storyline is not unreasonable, just as someone with a storyline of Provists beating up a Gallente tourist wouldn't be unreasonable.
Perhaps we could save our wrath for those who grossly offend?
EDIT: toned down some language and clarified some things.