Okay I have played a few of the storylines now and see a few issues with the companions and the concept of each storyline.

For example with the Jedi we understand that romantic activities by their nature cloud the Jedi's ability to reason and extract themselves and those around them from situation enough to weigh all options and understand that loses do occur. Hence as an example in the Jedi Knight storyline when Kira and the Knight kiss for the first time should Dark Points not tie in? as this would be the way to the dark side?

Or in the Sith (Light Side) with Ashara as she declares her love for the Sith.

So why does the system not create the issues?

Technically it doesn't make sense to do this, Satele Shan is even aledged to have a baby, the GRAND MASTER *pause for a pose for the credits) =P There has been a history of jedi reproducing and being married even, is has to be approved by the council though. In the case of Jedi Knight vs Kira it's a bit naughty , yes, but not unheard of. It's discouraged but not anathema =)

ED: Thinking on it I suspect bioware did a bit of canon digging to realise that. Even Luke Skywalker got married and had kids so did Leia, even if one did turn and kill her. At that point Luke was the new grand master I guess since he reinstated the jedi order singularly at the time on Yavin IIIV.

There is a lot of Canon in the universe but the deeper you dig the more you find it's interchangable and not at all final law. ~Hope it helps