Actually they did it pretty well.
Both my Knight and Consular are in loving relationships with companions and I earned ZERO Dark Side points.
You are most likely thinking of the two Padawan in love on Tython? Here is the rub... it isn't that they are in love and seeing each other that is wrong. It is that they are obsessed (at least she is) and they threat and bribe you into lying to the Jedi Masters to hide their more and more "Dark" relationship. The game got it right.
You take the Dark Side Flirt with Kira? Well it is because you are forcing romance on her in a vulnerable and inappropriate position. It is taking advantage. It is the only time you'll get a Dark Side point for romance so don't do it.
I was like, huh, you can get dark side points for romancing
Then I read your post.