The Three Lions won the Ashes three times in Flower's tenure and became the number one ranked Test side in the world, along with winning the World Twenty20 Cup.
Cook told BBC Sport: "I'm very proud of that era. I really only have fond memories of that, but I do believe it's kind of been tarnished and I'm sad about that.
"I think it's been a really sad week for cricket. We have to draw a line under it at some stage and this is a good time."
Pietersen also revealed that he do "anything" to return to the England side, despite being told he had no future with the team earlier this year.