You should be given lightside points when you do that. One less sand people makes a better galaxy. Just like when the Jedi hunted the Terentateks.
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You can do that without getting any dark side points, anyway.
Just ask enough questions during the "worthy of history" quest (where you get to talk to their story teller for the dragon pearl), and ask about the outsiders, and whether the similarity to their ancient selves they see is cultural or physical. And insist that HK ask. Make sure you have the best fighters there. You can wipe out the camp, loot everything, have far more gaffi sticks to take back for bounties, get the pearl back... and not get a single dark side point for it. After all, you were only trying to understand them better... :D
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Or you could just go through their stuff while your in their base, a lot quicker.