Dutchman Kramer, the overwhelming favourite to win his second gold medal at the Vancouver Olympics was disqualified after his coach sent him into the wrong lane eight laps from the finish while leading by a five-second margin.
"I wish it had not happened but it is a reality. Games are about triumph and defeat. I prefer it never to happen but it adds to the mystique of the Games.
"(If I were the team leader) the first thing I would do is I would say nothing," Rogge, who took part in three Olympics, said.
"I would let the rage out, recover, compose and then I would say he is the best skater of his generation.
"He is equal to Eric Heiden, Kees Verkerk, Johann Koss, Ard Schenk."
American Heiden swept the gold medals in all individual events at the 1980 Lake Placid Games, while Dutchmen Verkerk and Schenk won gold medals at the 1968 Grenoble and 1972 Sapporo Olympics.
Norwegian Koss grabbed three gold medals all in world record time at the 1994 Lillehammer Games.
"He is of that calibre. I suffer with him. He is still the number one and should go out and try to win a gold in the team pursuit," Rogge said.
The Netherlands are the overwhelming favourites in the men's pursuit.
"I know it is painful," he said, adding the mistake was unique for the Olympics. "There is nothing that comes to my mind spontaneously at the Games."
Four years ago American Lindsey Jacobellis denied herself the gold medal in the snowboard cross when she decided to showboat at the finish with an unnecessary jump, losing her balance and allowing Tanja Frieden to win gold.
"(Kramer's) is a little different to Jacobellis's. She made the error and it cost her dearly. Here the coach made the error Kramer did not make the error."