I love that the game is canon and I usually have a strong dislike for non-canon stuff.
I don't think that this is going to hurt the novel really. It doesn't really matter if she steals the RV after you've left her on the road or after you've let her go. Yes it changes the relationship between Lee and Lilly but I doubt Lee will be mentioned a lot. Even if it is I guess it's going to be quite vague. That will be the case with Larry as well.
Canon Lilly is the same as in the game. Her personality remains the same, it is just that you're seeing different aspects of it. A person doesn't just changes because you've been nice to them. Lilly changes a lot but that's due to events that always happen - Larry's death for example.
As for Shawn, there's no canon choice there. He always dies so it doesn't really matter if you've tried to save him or not.
thestalkinghead I was left with the impression that you wasn't happy with the choices in the game. What's with the nitpicking and canon worries?

I think it's actually quite the opposite. Those small things do not matter outside Lee and his group. They are irrelevant to the universe and to canon. They do matter, however, to the player, to Lee as a character and to their interaction with the rest of the characters.