The thing is, Samira, even in a lot of the EVE PF Amarrian slavery has been handled ham-handedly, depicting mostly the cruelty and injustice rather than any potential good. Then, any 'moralist' Amarrians get drowned out and eliminated by the power-hungry, as in the case with Arzad Hamri in the old days or the TCMC-favoring Holders winning out against more traditional ones. Then there's the nightmare of breeding slaves like they are cattle, eugenics and all (which should by all means be completely against the Amarrian faith), casually using slaves as disposable labor forces (again, immoral even to Amarrians) and blowing up planets when rebellions start (derp). This results in players seeing the faction as evil, and they play accordingly. 'Morally corrupt' slavery, even by the Amarrian standard, has been written into the background so thoroughly it would take a major reformation to root it out. Alas, I don't think the fiction team is interested in that at the moment.
Like I said, we might as well wear the mantle. The concepts of religion, slavery, authoritarianism and feudalistic social classism are always going to be seen as backwards to the average EVE player OOC, and only through suspension of belief (which many players lack, even RP'ers) would they be able to say 'Hey, they're not so bad!' No, the Amarr are bad from any sane modern person's view, and only people who drink the kool-aid IC (only Amarrians) think otherwise.
It's futile to struggle against it in any way but subtle pressures. You're in a highly stratified empire that wants to rule all of humanity through a singular religion to the exclusion of all others. Social structure and culture ensures that it will remain so for at least the next 100 - 1,000 years, much longer than the game will last. There are going to be tons of things a liberal/'nice Amarr' character is going to dislike, but they have to be patient and deal with it unless they want to become apostate or traitor.
As far as current affairs in the Empire, hopefully the story will flesh out more soon and we'll be able to clearly see who is reformist, who is extreme zealot, who is amoral power-hungry and who is the messianic ray of hope. I believe the slave raid will happen but that there are going to be a lot of people in the Empire who don't like it, maybe even the Empress. We'll have to wait and see.
Even so, despite the fact a slave raid might cause friction within the Empire, people outside of it are not going to care. The Empire did so-and-so and they're evil.
However, since I've given up on seeing the Empire do 'good things' in the cluster for a change, I would instead like the other factions get darker along with us. CCP has been doing a good job of this with the Gallente with the Black Eagles and creeper Roden. The Caldari are mixed, which is really refreshing and fascinating to watch. However, the Amarr/Minmatar conflict is still boringly black and white; crotchety old evil church slavers vs. romantically free space natives. If we're going to be mostly crotchety old church slavers forever, I want to be fighting barbarian savages with an ancient grudge that causes them to do some equally horrible, or even worse things. If we're going to be trying to enslave the Minmatar we should have a better reason than "because religion". Why not "enslave them because they're murdering our people whenever they can get their hands on them"? I really don't think the Minmatar military will be very restrained when it comes to Amarrian civilians. We already know they treat Amarrian POW's terribly, but the fact the Minmatar can be really cruel as well should be highlighted. Then maybe we can say all of the races are portrayed in a morally grey/dark grey light.
And before any Minmatar players say that the Republic doesn't have a dark side when it comes to Amarrians, I kick your sacred fern.
GOOD DAY.