You could do that!
Or, it might be corny/cliche, but you could always have them turn down being freed? Some kind of nice reply or minor reward for karmic goodness, but build something in that explains they can't be freed for whatever reason. Maybe their status as property protects them from past owners/debts/random vicious killers/whatever, or they'd just be enslaved again upon going off on their own, etc. That way you're 'thanking' the player for the effort but not removing the character arcs.
If you want to give an out to their arcs, I'd make it something crystal clear that you're skipping out on everything, won't be able to re-buy them or any other slaves, before the decision is made.
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They do have reasons to be slaves, so I have been considering this alternative too, where they only accept being freed after they have become comfortable with the protagonist (as it happens for both characters, if you are on the "right" path with them). Acknowledging it is important, since freeing them is one of those options which make sense. Even in the game's world, slavery is a rare thing, with specific laws and rules (when done legally), so it would be weird to not give the option, even if it's symbolic with no actual gameplay changes.