The term "Mary Sue" tends to be defined so broadly and inconsistently that it's become fairly useless as a term of criticism -- indeed, if the term is being applied to a character as far from the original definition as Grim Vargo, then it could potentially be applied to anyone. People seem to use it simply to mean "a character I don't like."
Strictly speaking, a Mary Sue is an impossibly idealized character who outperforms all the other characters and earns their undying devotion. None of that applies to Trys. She's a very flawed character who has a lot to learn from the other regulars and gets on their nerves a lot. If any new character in GTTS is idealized, hypercompetent, and highly popular with her crewmates, it's Jasminder Choudhury.
True, one aspect of a Mary Sue is that the author has a special affinity for the character (who's usually an author surrogate) and plays her up a great deal because of it. I'll admit, I'm very fond of Trys, and she does have a few author-surrogate qualities. But I did try to balance her with the other characters rather than making her too dominant. And I grew pretty fond of Choudhury too.
I am a massive fan of the Scottish writer Christopher Brookmyre, but the character of Jack Parlabane (Quiet Ugly One Morning, Country of the Blind, Boiling a Frog, Be my Enemy and Attack of the Unsinkable Rubber Ducks) is by that discription a Mary Sue charcter, but regardless of that, I bloody love him so not all Mary Sues are disliked.