Bringing this up again, because I finished Onderon yesterday after siding with Vaklu. I managed to do it without incurring a single Dark Side point, up to and including killing Kavar. Not one Dark Side point gained, I still had my Light Mastery after killing him, but Kavar still says I fell to the Dark Side.
What's more egregious about this is that despite it being possible to be full-on Light Side and side with Vaklu, you have to kill Kavar (unlike the aforementioned example in the OP about Vrook and the mercenaries) and as such you're still pushed into the Dark Side "You have failed me" speech at Dantooine and just have the bloodthirsty "I want to kill all Jedi" dialogue options.
But you still get Force Enlightenment.