I just tested the emerald turn-in. It works, but you only get 300g for turning them in, plus 200 xp. If you sell them both to the merchant he will give you 1500g.
Edit: I am not saying this is a problem, as choices are good, but if you sell them then you are left with an unfinished quest. It's a minor quibble. I think those emeralds are unique but I am not aware of a simple way to detect a player selling them.
Edit 2: I think the emeralds should be marked as stolen. Wait, is that a thing in BG? Will merchants refuse to buy stolen items? The emeralds would be an obvious choice as many people already know about the theft and the bounty. I can't see the Nashkel merchant paying 1500 for such obviously stolen goods when there are guards marching back and forth in front of his door who are looking for the thief.
Edit 3: So apparently there is no "stolen" flag in the Infinity Engine. Here's an idea: Mark the emeralds as critical so they cannot be sold. Then, as soon as the emeralds are both taken down, one of them starts a conversation with the player, to the effect of "There is a bounty on these emeralds" with responses being "I should turn them in to the magistrate" or "I could probably get more selling them, though I will have to sell them at a discount." If the second choice is selected, then the quest log is updated and the emeralds are replaced with sellable versions that go for much less; say 300 each.