I think it becomes a whole lot easier if you have two alignments for each character or organisation - Intentions and Methods. For example:
Amarr Empire
The Amarr Empire generally believes that it's helping the world by spreading its religion, but the methodology by which it approaches this task causes immense suffering. However, it approaches the torture and enslavement of millions with the same organisation and rigorous bureaucracy it would approach civil management. Whatever else you call them, the Amarrians are far from disorganised.
Intentions: Lawful Good
Methods: Lawful Evil
Minmatar Republic
The Minmatar Republic, at heart, just want to free their people from slavery and be left in peace. They are, however, willing to go to any length and perform acts of extraordinary violence to get their way, but they've never quite let their intentions sink to all-out retributory genocide - yet.
Intentions: Chaotic Good
Methods: Chaotic Neutral
Gallente Federation
At heart, the Gallente Federation's core ideals are pretty much the very definition of Neutral Good - have a set of laws that's just strict enough to protect people from each other, but maximise personal freedom. The methods they use to defend their freedom, however, generally follow a strong consequentialist ideology - the end can justify the means. Most Gallente believe that while this philosophy is largely true, it has its limits - but some more fanatical defenders of the Eagle do not.
Intentions: Neutral Good
Methods: Generally Neutral, extremist factions tend to be Neutral Evil or Chaotic Neutral
Caldari State
The Caldari State might just be the "purest" of the four main factions, because while the ideologies of its intentions and its methods might not really match, most of the ethical and moral standards behind them do. At heart, the Caldari believe that a man's successes define him, and that success is success, no matter what shape it takes. That said, there are a few lines one shouldn't cross, and a few things that just aren't done. To the Caldari, good and evil are useful theoretical concepts, but trust and honour are very real and tangible things.
Intentions: Lawful Neutral
Methods: Lawful Neutral
Blood Raider Covenant
The Blood Raider Covenant's ideologies aren't that objectionable in and of themselves. Most people who aren't Amarrian religious hardliners object to the Covenant not because of what they believe (after all, there are far weirder religious cults in the world of EVE), but because of the really rather nasty things that they do.
Intentions: Chaotic Neutral
Methods: Chaotic Evil
Sansha's Nation
Sansha's Nation, to the pragmatic, has never really looked like anything other than a vanity project. It's one man's dream to rule a world of cybernetically lobotomised humans slaved to his will. The thing is, his dream was of a society so ordered that free will would become obselete, whereas his recent methodology has been ludicrously insane and seemingly designed to cause as much panic and chaos as possible.
Intentions: Lawful Evil
Methods: Chaotic Evil
Intaki Syndicate
I strongly believe if there was such a concept as "Aggressively Neutral", the Intaki Syndicate would epitomise it.
Intentions: Neutral
Methods: Neutral
Equilibrium of Man
They quite literally want to destroy all sentient life, and every action we've seen them take has been in service of this goal. What more need be said?
Intentions: Chaotic Evil
Methods: Chaotic Evil
Andreus Ixiris
Andreus strongly believes the only morally acceptable society is one that gives its citizens as much personal freedom as possible, and that the Federation is by far the closest to achieving this goal. There's very little he wouldn't do to defend it, no matter how morally questionable it was - but he wouldn't perform them for simple personal satisfaction. He'd have to know there'd be some tangible benefit to the Federation.
Intentions: Chaotic Good
Methods: Neutral