"How to fix slavery without murder" is a serious problem in the real world as well. You can find Antislavery International's answer here:
http://www.antislavery.org/homepage/antislavery/about.htm
That's the slow, realistic, long term way of going about things.
Historically, most people's answer to the question has been "Its not murder if its war" A lot of otherwise pacificistic Northerners cheered when John Brown attack Harper's Ferry, there are other examples floating around. That said, there's a big difference between slitting someone's throat in the middle of the night and a decleration of war.
Notably, "fair warning". If the characters want to be Lawful, or maybe even Good, they should warn the people about what they're going to do, and hopefully get a legitimate authority to sanction it. If you have a high ranking Cleric in the group, he can probably order the killing done in the name of God (presuming that you give fair warning, and that his god approves of these kinds of things.)
If the characters slip in during the night, kill everyone in the place, and then slip out with the slaves, well, it may very well be ethically justifiable. But lets not pull any punches: the word for that sort of behavior is terrorism, and they're going to make the entire country hate them. They may very well be able to escape unscathed, they may very well be right to oppose the country, but its still going to feel really quesy.
There may also be magical ways around this. Really obscene Diplomacy rolls, Mass Charm Person, Teleportation circle - not anything the player's are likely to have, but they exist.
Goodluck. I think this is an awesome scenario.