Your definition of Mary Sue is off. A Mary Sue is not defined by how many flaws he/she has. Many bad authors try to add superficial flaws to their characters in an attempt to make him not a Mary Sue. (i.e. Ugly, "boring" personality, etc.)

A Mary Sue is defined by what she DOES to the story and other characters. If she warps the story around herself, she's a Mary Sue (or a Gary Stu/Marty Stu for males). To take a simple example, Bella Swan from Twilight. Boring, no personality, little liked in her old school, suddenly becomes the object of affection for a vampire and werewolf. (...Or so I hear. I only read the TVTropes articles on it. I never read the books. Really.)

Under this definition, Thrall, who does indeed have enemies (some of whom aren't exactly wrong in their views) and has made a host of mistakes, is not a Mary Sue. The story doesn't revolve around him or his exploits, and he doesn't single-handedly kill Old Gods. Now, if Cataclysm were to entirely be about how he kills Deathwing and fixes the entire world... Yeah, then he'd be a Mary Sue.