Let's not forget that many people peak later.
Do I think Rojas will ever be a star sprinter? No. But he could mature into somebody for hilly classics. Think it's a bit too early to write him off as a journeyman, especially given some of the rides he's put in recently, such as climbing with Andy Schleck in the Tour de Suisse, and of course the Caisse 1-2 from the race last year, when Costa got the win. Rojas is more of an all-round guy than a pure sprinter à la Cavendish, and that's hurt his results. He can be competitive and score points in a much broader range of events, but Cavendish is the outright best at one of those events. Not to mention that Rojas is racing for a team which has, until this year, been predicated primarily on GCs, and so he's been given precious little support in his quest for wins and has often not raced as many events that go to sprints as many other sprinters - if he had a team that cared more about sprints (before 2011) and went to more events, maybe he could have more wins. But he doesn't. Some of it's to do with his physical limitations, some of it's to do with race calendars and team focus.
Besides, Thor Hushovd won the green jersey without a stage win in 2005.
If Mark Cavendish wins the green jersey, which is more than likely, he deserves it, because he's been the best sprinter in the race by a country mile.
If José Joaquín Rojas had won it, which is fanciful at best, he would deserve it, because he managed to find a way to win despite a system which didn't play to his strengths.
The points system has its strengths and weaknesses. It suits some riders better than others. But you can only win on the points system in place at the time.