No.
Does winning on time give less points than winning by checkmate?
i suppose the question is "should winning on time give less points than checkmate?"
That is certainly a question, though not a question that I was hoping to have answered. If winning on time did give fewer points than a checkmate, that would leave open the potential of abuse, i.e. people would intentionally run out of time rather than resign or face checkmate.
Sometimes I'll be playing someone (as is the case in this game: http://www.chess.com/livechess/game?id=667201141) and instead of resigning or letting me win, they'll simply make me sit in the game until their time runs out (sometimes 20 minutes or more!)
Does this mean that I gain fewer points because I didn't win by checkmate? If so, that's a major flaw