No, because then Nia would be tsundere and not a mary sue. The basic definition of a mary sue character is basically, "the perfect women without flaws"
And really, Nia was almost to the T, the perfect girl/women. She was kind and bubbly and loved everyone. She didn't even really hate Genome or his minions really, not without a very good reason. She was accepting of pretty much everything at the beginning, and do anything for Simon.
When I think of mary sue, I always think of Tohru from Fruits Basket.