I don't have advice, but I just wanted to say that I would have felt the same way you did. It would upset me because he was with his age peers acting like his age peers! It was wrong, IMO, for the teacher to hold him to a different behavior standard than the other kids based on what he will be doing academically in the fall. This is a summer program and is probably designed to be a little more laid-back than school is supposed to be. He needs to be able to act like a 6 year old when he's with 6 year olds -- that's called social awareness and empathy. His size shouldn't matter one bit either, although I know from years of experience with my super tall kids that people expect them to act as old as they look as opposed to how old they actually are. That's not fair of this teacher to expect different behavior from him because he happens to look older.
FWIW, my two gifted kiddos are masters of fitting into the groups they are placed into, whether that's age peers or friends and academic peers years older. I wouldn't expect, based soley on him acting his age with agemates, that your DS will have any trouble meeting the standards in his 3rd grade class in the fall. If you do find that your DS gets pulled in by the less-than-stellar behavior of a classmate, though, it's often easy enough to ask the teacher not to sit them near each other.
And I get that it will be important for your DS to fit in socially and meet the behavior expectations of his third grade class, but I just don't think that he should have been called out in this particular situation.
