Both the 33-year-old Pietersen, who finished as the tourists' top scorer in the series despite managing just 294 runs at a rate of 29.40, and Flower did their best to rubbish the reports in bland public statements. (Agencies)
But it seems new England and Wales Cricket Board (ECB) managing director Paul Downton will have to decide if the talented shotmaker remains 'worth the trouble'.
According to former England seamer Mike Selvey, the long-serving cricket correspondent of the Guardian, Flower's view was clear.
"So adamant is Flower that the presence of Pietersen in the dressing room is detrimental to the future development of the side that he is believed to be prepared to resign his position should Downton, James Whitaker, the new national selector, and Alastair Cook -- if he retains the captaincy -- insist that Pietersen should be a part of that process," Selvey wrote.
There is also the question of whether Pietersen's chronic knee injury means his best days are now behind him, despite his stated desire to score 10,000 Test runs -- a goal which, if he reaches it, is likely to help, not hinder, England's prospects.
Indeed Pietersen's maiden Test century has a claim to being England's most important of the 21st century so far, given that it secured the draw that saw England regain the Ashes after an 18-year gap in 2005.
On a day when conventional 'bat for a draw' tactics simply led a to a flurry of wickets at the other end, Pietersen audaciously counter-attacked bowlers of the caliber of Glenn McGrath, Brett Lee and Shane Warne.
And in Mumbai in 2012 he made 186 against India on a spinners' pitch where most batsmen were struggling just to stay at the crease.
England's desire to have a captain across all three formats saw the lanky shotmaker given the job in 2008. But a falling-out with coach Peter Moores -- not to mention his then assistant Flower -- meant Pietersen's tenure lasted barely five months before both men lost their posts.
Last year's Headingley Test against South Africa encapsulated Pietersen's England career.
Having produced a match-saving century where Dale Steyn and Morne Morkel were treated like club bowlers, Pietersen gave an equally stunning post-match press conference in which he proclaimed, "It's tough being me in this dressing room".
The comments chimed with the idea of Pietersen the mercenary, after he clashed with England's management over his desire to play more often in the lucrative Twenty20 Indian Premier League.
Soon afterwards it emerged he'd sent "provocative" texts allegedly critical of then England captain Andrew Strauss to South African players. Pietersen was briefly dropped by England, only to be recalled when Cook took over following Strauss's retirement.
Few people were more admiring of Pietersen's innings at Headingley than Geoffrey Boycott, coincidentally the most controversial England player of his generation, although in his case he faced accusations of not being a team man on account of scoring too slowly.
Roll on a few months, and Boycott was calling Pietersen "a mug" and all the top order "one-day clowns".
There is a case for saying a truly great batsman would, at least at some point, have found a way to steer a middle course. But, as former England captain Mike Brearley once wrote, it's wishful to think a tortoise can ever jump like a gazelle.
And after the Sydney thrashing, Michael Vaughan – the first England captain Pietersen played under -- said: "I hope England do not take the easy way out of this mess by making Kevin Pietersen the victim for the Ashes whitewash."
Both the 33-year-old Pietersen, who finished as the tourists' top scorer in the series despite managing just 294 runs at a rate of 29.40, and Flower did their best to rubbish the reports in bland public statements.