I also agree that, despite its etymology, "Mary Sue" doesn't necessarily have to come with a negative connotation. Much like "canon" (to reference another current thread about terminology), the term can be used descriptively without suggesting on its own that a character is well- or badly-written.
But really, that's the problem. There is no consensus about what it means. Many people do
use it in a derogatory way, while others don't. And there are countless different ways of defining it. So using the label tends to create misunderstanding rather than clarity. That's another reason I resist using it if it can be avoided.