What makes you think the Starks are the good guys? And let's not forget that, as far as those of you who haven't read the books know, there are still a lot of Starks alive: Jon Snow, Bran, Rickon, Arya, Sansa.
What I like about the books is that the characters evolve (or devolve) throughout - Jaime becomes more likeable, even heroic at times (and already displayed this in the TV show when he jumped into the pit with the bear). Tyrion is by far my favorite character in the book; the most complex, and the most "human." Arya is my second favorite. She is a total bad ass.
But we still have some "clear" heroes - Daenarys and Jon, specifically as far as the "big" time players. The Onion Knight, The Hound as smaller ones. Although The Hound is also a very complex character he seems to stick true to his oath as a knight most of the time.
There is still a lot of story from book 3 left to tell. Some good stuff to come.