Landing on Tatooine, I ended up with a bunch of Gizka on my ship. I already saw Gizka poison at a trader, so I could get rid of them. But then again, I'm a light side jedi (at least for now), so what's the most "good" procedure to deal with them? Do they pose a threat at some point or can I just let them hop around?
You do not gain any Dark side points for dealing with the Gizka infestation with poison.
However there is an alternate way to handle it, on Manaan there is a person who can take them off of your hands. But if you don't take either of those actions near the end of the game they will just leave.