Non linear is good if the rewards are comparable for every path you take. In the case of Mary, the other paths are just for those that don't read the dialogues or don't want to follow good advice.
Just like in life.
The best example from SDTHEO of a quest with different paths possible is False Trace. Some chose to help the pirate's wife, because they "could not refuse a women that asked for their help", I liked to chose the lesser evil and that pirate was just like our character, a pirate, he didn't deserved to be punished for wanting his wife back, while his wife it was revealed in one of the paths to be a liar, treacherous, bloodthirsty and manipulative person. More dangerous than her husband. In fact, there were hints about her character from the moment she started talking.
So, everybody must have thaught they made the right decision, some for helping the woman, some for helping the pirate, some for punishing both.
That's amazing writting for such a small side quest with these subtle hints about what is wrong and what is right.
Dutch Gambit too, working for Lucas, we get the idea after a while that the guy is evil. The other two sides, the secret organization and the English privateer are most likely just other shades of gray.