Actually, your choices did affect the way the game played throughout.
People seem to keep overlooking little things that change depending how you act. People are so fixated on the "Dark Jedi/Light Jedi" thing and overlook other things. For instance, on Taris you have a choice of working with the Vulkars or the Beks. If you choose one, you have to fight the other. In other words, your "choices affect the story", because if you choose DS, you side with the Beks and have to kill the Vulkars. If you choose LS, you defeat the Beks.
So to use your comments, your hypothesis is in fact incorrect.
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Wait a minute... weren't you LS if you sided with the Beks and DS if with the Vulkars?