I'm going to have to disagree with some of the people here. If anything the SI storyline favors the LS path, mostly because of Ashara.
If you expected to be able to defect to the Republic you were obviously going to be disappointed (no classes can defect to the other side), and if you wanted to play a character that liked the Republic and hated the Empire you should have rolled Jedi.
My Sith Inquisitor saw some good in the Sith Order, even though there's also a lot of bad. He wanted to reform the Empire to make it more ethical (and your talks with Ashara really focus on this).
One thing I loved to do was when my character would cite parts of the Sith Code to justify doing LS actions.
A LS SI is all about finding an ethical way to follow the Sith way of life. It's really fascinating.
You also end up in a really good place for a reformist sith in the end (though it also works well with being a power hungry DS Sith). In the end you