In an interview with the BBC's Test Match Special, due to be broadcast during lunch on the opening day of Cook's final Test at The Oval on Friday, he admitted that he had not initially wanted Pietersen's exile to be permanent and feels the episode was poorly handled by the ECB.
But, while insisting he had "never fallen out" with Pietersen he also accepted he was relieved when Andrew Strauss was appointed director of England cricket and ended any uncertainty over Pietersen's return.
The Pietersen debacle started, in earnest, in 2014. After a grim Ashes tour, which England lost 5-0 under Cook's captaincy, the ECB management decided that Pietersen should be dropped. While Cook, who had fought for Pietersen's recall ahead of the 2012 India tour, did not favour a permanent exclusion, the director of England cricket, Paul Downton, was adamant it was for the best.
But the permanence of the decision was not fully spelt out and Cook was left to bear the brunt of the criticism.
Then, just as the furore was dying down, the ECB's new chairman, Colin Graves, appeared to offer Pietersen hope of a recall sparking new speculation over the situation. It was not until Strauss succeeded Downton, after the 2015 World Cup, that it was clarified that there would be no way back.
"It was the toughest time of my career and there's no doubt that it was affected my batting," Cook told the BBC. "The day when Straussy came out and said Kevin wasn't going to play for us anymore, that was a massive weight off my shoulders.
"I was involved in the decision at first, but the England captain doesn't have the final say on hiring and firing. I agreed with it, but I said 'why don't we give him some time off, we can go away and maybe KP can come back later on'.
"Paul Downton wanted clarity, a clean break, because people would always be asking when is he coming back. You had to back his decisions because that's what his job was. The fallout was pretty nasty and I don't think the ECB handled it well or appreciated how social media worked very well then. I bore a lot of the brunt of it. I suppose that's what being captain is.
"Graham Gooch will always be responsible for the [dropping of] David Gower thing. I don't know the details of that, but it is something he is always associated with and I will always be associated with the KP one.
"I would refute anyone saying that I was the one that chucked him down the stairs, but I was involved in the decision and I believed it was right at that time. What could have happened a year later, I don't know. Looking back, I can safely say all the decisions I made were done for the best of the England cricket team at that time. On that one, there were a lot of other people, way above my head, also involved in it. I felt like I was being left alone as the captain."
While Cook and Pietersen have not spoken for four years, Cook accepted they "created some amazing memories" together and hoped that time can prove to be a "great healer" in their relationship.
"I haven't spoken to him since that day," Cook said. "But I think time is a great healer. We spent a lot of time together and created some amazing memories.
"The thing is, we never fell out. Since then, the internet has fallen out for us. As two blokes, if you take cricket out of it, we have never fallen out. He will have a different opinion, I'm sure."