I don't see why undersized would make him worse. He has huge wingspan, is extremely quick, athletic, and fast and he clearly has a passion for defense which is huge thing to go along with that. There are very very few guys in the league that pride themselves in defense.
The only potential problem regarding size would be a dominant bigger 2 guard I think the post maybe Kobe, joe johnson, or Dwade. Other than those guys I don't see why anyone would ever be worried about his size. I think Rondo would probably be better defensive player at the 2 than 75% shooting guards cause the fact is there aren't many good defensive players