Speaking for the first time since the release of Pietersen's book 'KP', Cook refuted the sacked batsman's allegations of a bullying culture in the England dressing room and said the furore caused has damaged the sport.
"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," Cook told the BBC on Saturday.
"International cricket is a tough place and, as a team, you're striving for excellence at all times.
"Certainly at some stages those frustrations boiled over more than they should have done, but that was only people who were desperate to succeed and wanting to know the other 10 blokes around them were committed 100 percent to it also.
"Did it overstep the mark a couple of times? Possibly, but we addressed those issues. That's what happens in teams, but it certainly wasn't a bullying environment as such," he added.
Pietersen was axed following the 5-0 Ashes defeat in Australia at the start of the year, with England inferring the South Africa-born batsman was not a team player.
Both he and Cook were part of the test side that topped the world rankings in 2011 under former captain Strauss, who led the team to back-to-back Ashes series wins.
Cook then captained England to another Ashes win last year under the guidance of their now former coach Andy Flower, who has come in for heavy criticism from Pietersen.
"I am very proud of the era I have played in. To win three Ashes, to become the best side in the world, to play with some great players. I really only have fond memories of that," Cook explained.
"I am incredibly proud to have contributed in that period. To play under Andrew Strauss, to have played under Andy Flower as coach, I have only got respect for these guys. I do believe that era has been tarnished, and I am sad about that."
Pietersen, who played in 104 Tests for England, labelled Flower as a "mood hoover" who was "contagiously sour" and "infectiously dour" in the book that went on sale on Thursday.
The 34-year-old batsmen also blamed this year's humiliating Ashes whitewash in Australia on Flower but Cook said he and his team mates refuse to accept Pietersen's view.
"I've known Andy since he was a player in the Essex dressing room", Cook said.
"He took me under his wing as a player and then obviously, your relationship changes as a coach to a player and then to a head coach and a captain. I've only got respect for him, as a man, as a coach.
"Chatting to some of the other players about it, they feel the same. A lot of our success was down to his drive and his determination to make us a tough England side."
Cook is most shocked by Pietersen's criticism of now deposed wicketkeeper Matt Prior, who is labelled in the book as "back-stabbing".
"Matty is a great man and has been a fantastic servant to English cricket," Cook explained.
"He has to be remembered as a guy who put his heart and soul on the line for England. The team was all that mattered to him."
(Reporting By Sam Holden; Editing by Ian Chadband)
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