BOSTON — It seems incredible now, but there was a time, just over two years ago, when the Red Sox weren’t sure if they wanted Josh Beckett.

Or, more to the point, whether they wanted him as much as A.J. Burnett.

In November 2005, having been unceremoniously swept by the Chicago White Sox in the ALDS, the Red Sox recognized the need to upgrade their rotation. At the winter meetings, the Sox front office was pleasantly surprised to be approached by the Florida Marlins and told that Beckett could be had in a trade — for the right price.

At the time, Burnett, Beckett’s teammate with the Marlins, was on the free-agent market, providing an alternative choice for the Sox.

Both were powerful right-handers with the potential to be front-of-the-rotation starters. But while Burnett was available to the highest bidder, Beckett would have to be obtained at the expense of several top prospects.

General manager Theo Epstein had left his post on Halloween night in something of a power struggle, leaving something of a leadership vacuum in the baseball operations department. In his absence, the organization operated by committee and in internal debates, principal owner John Henry, who knew both pitchers in his time as Marlins’ owner, was the loudest voice for Burnett.

It wasn’t that Henry thought Burnett was necessarily the better pitcher, or that Beckett would be a failure. Henry was merely looking at his options as a businessman, and in a cost analysis, decided that all things being relatively equal, the Sox would be better off spending money for Burnett rather than spending prospects to land Beckett.

A source who was familiar with the discussions said this week that had the circumstances been reversed — that is, if Beckett had been the free agent and Burnett available only via trade — Henry’s preference would have been reversed.

“My partners don’t like it when I talk about this,” said Henry, smiling, when asked to recount the debate this week. “But your (account) is accurate.”

Henry’s chief objection was that the Sox would be forced into surrendering shortstop prospect Hanley Ramirez in the swap. From the beginning, the Marlins told the Red Sox’ that Ramirez’s inclusion was non-negotiable.

With the benefit of hindsight, of course, the Sox’ reluctance seems baffling. Burnett has been an underachiever for the Blue Jays, who signed him to a 5-year, $55-million deal. Just weeks before that, the Sox dealt Hanley Ramirez, Anibal Sanchez and two other pitching prospects for Beckett, Mike Lowell and Guillermo Mota.

He was 10-8 with a 3.98 ERA in 2006, but missed a third of his first season with the Blue Jays. This past year, again shortened by arm issues, he was again 10-8 with a 3.75 ERA, making 25 starts.

In two seasons, then, Burnett has won as many games as Beckett did this season alone. Worse, Toronto general manager J.P. Ricciardi, who gave Burnett his landmark deal, felt the need to publicly question his pitcher’s toughness when Burnett took longer than anticipated to come back from some shoulder soreness.

No one has felt the need to question Beckett’s intestinal fortitude in Boston.

To the contrary, Beckett has this October solidified his reputation as one of baseball’s best big-game performers. He opened his third straight postseason for the Red Sox last night and improved to 6-2 in his career.

It’s clear that his starts in the 2003 NLCS and World Series — when he was named World Series MVP and defeated the Yankees in Yankee Stadium on three days’ rest — were just a precursor to this fall’s standout work.

In Toronto, meanwhile, Burnett continues to be regarded as a guy with great stuff who doesn’t win as much as he should.

Ramirez, chosen as the National League Rookie of the Year in 2006 and who finished tied for third in the N.L. batting race in this, his second season, has turned out to be every bit as good as Henry projected.

It’s doubtful, however, that he regrets being overruled. Not with a second World Series title three wins a way, due in large measure to the pitcher who wasn’t his first choice.

smcadam@projo.com