The old D&D alignment systems don't tend to work too well in shades-of-gray (or rather realistic) worlds. In fact, I've banned alignment from all my campaigns, since once you put an alignment system on most characters, people start behaving like they're chained by it.
Merdaneth is obviously Lawful Good for example:
A lawful good character acts as a good person is expected or required to act. He combines a commitment to oppose evil with the discipline to fight relentlessly. He tells the truth, keeps his word, helps those in need, and speaks out against injustice. A lawful good character hates to see the guilty go unpunished.
That is 100% applicable to him.
He tries to follow what the Amarr traditions and society says a moral person is excepted or required to do. He opposes evil and fights relentlessly. He never lies, is friendly to those in need, and speaks out against injustices. And he certainly wants to see all guilty people punished. Just what is just and unjust, and good and evil to him is different from many others.
From his viewpoint most of the Matari terrorists he fights are Chaotic Evil:
A chaotic evil character does whatever his greed, hatred, and lust for destruction drive him to do. He is hot-tempered, vicious, arbitrarily violent, and unpredictable. If he is simply out for whatever he can get, he is ruthless and brutal. If he is committed to the spread of evil and chaos, he is even worse. Thankfully, his plans are haphazard, and any groups he joins or forms are poorly organized. Typically, chaotic evil people can be made to work together only by force, and their leader lasts only as long as he can thwart attempts to topple or assassinate him.
In his opinion they attack the Amarr out of lust for destruction. They are quick to anger, ready to kill innocents for their cause, lie if it suits their 'greater purpose' and trying to destabilize Amarr society is the very epitome of trying to spread evil and chaos. Fortunately, the Tribals are haphazard, poorly (non-centrally) organized and their hatred easily turns inward when not opposed by a strong target. Portioning out parts of Providence to belligerent allies with the purpose of turning it into some kind of a 'Fight Club', centered on murder, brutality and destruction is *the* proof that Ushra'Khan are a Chaotic Evil organization for example.
Star Fraction as an organization tended to be neutral evil although Jade. Use rules and principles only if it works to your advantage:
A neutral evil villain does whatever she can get away with. She is out for herself, pure and simple. She sheds no tears for those she kills, whether for profit, sport, or convenience
That was the typical Freecaptain for you from Merdaneth's point of view.
Gallente society: Chaotic Neutral.
And so on and on.