As far as slavery being evil, let's take a step back and look into history. Romans had slaves, and didn't consider it evil. Greeks did so too. All european societies of the XVth to XIXth century had them too. And many more other examples exist. Why did this happen? Because slaves suffer a process that turns them from people to objects: romans and greeks considered the others barbarians who weren't as important as them; europeans considered slaves as lacking soul, so they didn't have rights nor will.
So, if we take a look into the Amarr, we see such a process exists as well. Slaves have souls, but they've spent them in the wrong way. They being so wrong makes them under-persons, not full people, because they aren't in the light of God. To an extent, they are barbarics like the romans thought of their slaves, and soul less like the europeans did. They are like intelligent monkeys to the Amarr: they can be taught with carrot and stick and eventually they will end up understanding the true nature of God. Then they will be full persons and accepted into the fold of society.
And why would they leave it? Sure, eating pork is an irrational taboo so its a matter of faith, but that is not the case with slavery: of all the attempts by the Amarr, only the Minmatarr were a failure, and them only to some extent, as the Ammatarr show. So, as far as the amarrian go, slavery actually works in uplifting "animals into people". So, obviously, it can't be bad! They are better now than they were! So, as Lallara pointed out, the Amarr haven't chosen this path out of ignorance (they are the first space-faring nation afterall, they are quite technologically and ideologically advanced in their own road), they chose it because it works, it gets the job done.
As for the Scriptures being unmovable, you already provided more than enough proofs that such a thing is not true. The Empire changes like every society to adapt itself to the needs of the times. Taking another real-world reference, the Catholic Church has reformed it's own dogma in every Concilium it has had until the last one, and not in minor details: they added books to the Bible, they decided that the Pope was infallible in matters of religion, that the Virgin was virgin, etc. This is because the Bible is a book written by human prophets trying to transfer the message God gave them. This doesn't happen in muslim religion, for example, because the Koran is a sacred text handed down directly by God, so it can't be changed and is subject to many rituals the Bible is not.
IIRC, the amarrian religion is closer to the Bible in this matter than the Koran, and so it is only natural that it adapts to new situations. Not only does it include new scientific discoveries (all science is part of the amarrian Scriptures), but it would probably revisit events and ideas from the past. The pork taboo would probably be thrown out once there is no reason for it, when the TC got into looking at it and seeing they need no longer to protect themselves from those bacteria. The whole Tetrimon story arc was very clear on this, as very different Scriptures (supposedly older and, thus, closer to the original truth) were brought to the Empire and could have had Empire-wide vast consequences. So all can change in the amarrian faith as long as enough time passes by, even in RL there have been dogmas added to the Catholic faith that didn't exist as first as such (the Virgin being virgin, for example), and dogmas are the most central element of any religion: those tenents that, if you don't share and believe deeply, you can't be considered a member of said religion.