Can you define 'Mary Sue' in this context?
My understanding of the concept is that a 'Mary Sue' is an idealised character/author insert, and neither really seem applicable to Clara (as far as I can see anyway
). Clara is the Doctor's companion, and a lot of stuff in Doctor Who has always involved the Doctor's companion, and they often help to save the day. She's just a main character.
A main character helping to save the day doesn't seem exactly unusual.