Thats the thing.
Lets take an example that is not from real life or from EVE.
Lets take the factions of one of my favourite sci-fi games of all time, Alpha Centauri.
Each and every faction has their own flavour, each faction gets their pros and cons from that flavour.
In the beginning of the game (or the history of the faction) only thing that the faction competes against is their natural surroundings.
Flourishing in a hostile environment is the first hurdle for all of them, each approach the dilemma in a different way and each and every one of them develops in a way that is suitable to their flavour, the pros and cons they have and according to the resources that they have at hand.
Next hurdle is encountering the first faction they encounter, how to keep them from attacking you, are you compatible, can you live in peace, do you need a large military to deter the possibility of attack, can you trade, can you become allies, can you just buy their friendship, will they betray you in the long run, will you pretend to be their friend and leech their resources and tech etc.
Then the whole thing goes global, you have to balance it all with all the factions and keep your back covered against the alliances of your peers and try to thrive in a hostile environment with potentially hostile other factions, which all have their flavours and ways of dealing with things.
In the world of Alpha Centauri you can get extra content with the Alien Crossfire, which adds two alien factions on the planet (also a lot of new player faction options arise) that are not interested in surviving on the planet, but taking control of it, by fulfilling their own goals (they have to gain access to some artifacts that enable them to control the whole planet and win the game.) They have higher tech level, they are hostile, and they would rather kill you than talk with you. Which adds a little bit of more flavour to the whole pot.
The point that I am making, in the beginning each and every faction is completely concentrated on survival, there is no moral issues involved in developing into a faction that survives/flourishes in a hostile environment, but it means that each faction creates their own morality while doing so (different choices in how you run your faction affect how other factions see you, friendly or an enemy.)
This is where it crosses over with EVE, each faction has flourished in a different kind of environment and has developed their own way of doing things, their own morality. None of them are good or bad, they have just made choices based on their 'flavour' during their path into an Empire, their morality is pretty much based on the conditions that the faction had to survive in after the collapse.
The problem is the factions that have risen _after_ the collapse.
Their development of morality consists of being in a universe where there is these big entities that you can feed upon, the option of being a parasite is part of the picture (you could argue that Amarrians are parasitic, but if you do, then you know nothing about the motivations of the Amarrians and their way of doing slavery.)
In these smaller factions their morality has developed on a completely different set of rules for survival than with their predecessors.
Which will naturally make them OOCly much more morally reprehensible towards a well socialized individual because they thrive on the suffering of their Fellow Man.
Only exception in the smaller factions are the Thukkers, they have developed in the Minmatar tribal structure and continued their own development when they gained the ability to travel in space, they are 'morally sound' in the way that the other smaller factions are not, because they lack the parasitic aspect of the other smaller factions. They may be a little dodgy, but that is only because their survival mechanisms are similar to the opportunistic Travellers/Gypsies of the real world (or Jawas of the Star Wars universe) where the law of possession is different for them.
But I am rambling, better go hunt for brekkies.