Pye was in overall charge of the mission, not Fletcher. He was the guy who called a halt to the run for Wake. Here are couple of exerts from American Heritage Magazine. First, a description of Pye and his taking command from Kimmel on the 15th of December:
"Pye was a careful officer. Nimitz, the kindest and most gently spoken of great war admirals, once described him as a "great brain but no guts." In an operation where other men saw opportunity, Pye was the sort of man who naturally saw difficulties. In looking over the operational plans of the departed Kimmel, Pye saw difficulties aplenty. In a single gambler's toss Kimmel, who had lost much of the Pacific Fleet in one afternoon, was sending the rest of it piecemeal into waters that the Navy did not control to engage an enemy whose position and strength he did not know. No, Pye didn't like the plan at all. Prudently he ordered Admiral Brown's Lexington to turn north away from the Marshalls to give Fletcher closer support. "
Second, the situation that lead to the recall orders:
"There was not much doubt in Pye's mind any longer. He had never liked the plan in the first place, and Cunningham's message indicated it was too late to relieve Wake anyway. But should he let the Saratoga force sail on and engage whatever enemy could be found? Pye didn't like that idea much either. A captain sailing into a sea battle ought to have some idea what he was getting into, but as one staff officer commented, "we had no more idea than a billy goat" what was going on at Wake. Pye radioed Fletcher, telling him to break off and return to port.
Fletcher was 425 miles from Wake when he got Pye's message. His task force had already suffered several frustrating delays. Had Fletcher made straight for Wake, he probably would have arrived about the same time as Kajioka, but not wanting to steam into battle with half-empty destroyers, he had paused to refuel. The refueling was snafu from the start. Seven oil hoses ruptured, and a number of towlines parted in the rolling seas. In ten hours only four destroyers were filled while the fleet actually drifted farther away from Wake. During the voyage Pye sent Fletcher a series of conflicting dispatches, each more cautionary than the previous one. It is likely Fletcher was glad to finally get a direct, explicit order from Pearl Harbor. He complied swiftly."
Lastly, the situation onboard the ships when Pye's order came through.
"The American people did not know a fleet had been ordered to Wake until much later, so there was no public reaction to the withdrawal. But within the Navy and Marine Corps, the reaction was immediate and bitter. Officers on the Saratoga, some of them weeping, pleaded with Fletcher to put Nelson's blind eye to the telescope and sail on in spite of orders. The talk became so heated that Admiral Fitch left the bridge of his own ship because he did not want officially to hear his officers speaking in terms that were close to mutinous, particularly when they expressed sentiments he agreed with. One officer aboard the Enterprise scribbled furiously in an unofficial log, "It's the war between two yellow races."
The incident marred Fletcher's long and honorable naval career. He was frequently referred to thereafter as "Fueling Jack Fletcher" and chastised for lack of resoluteness in combat. In fairness Admiral Fletcher did not win the Medal of Honor because he was squeamish about fighting, and to divide one's forces in the face of a numerically superior enemy, as he was to do five months later at the Battle of Midway, is not the mark of a timid admiral. The worst that can be said about Fletcher is that he was not Nelson."
The entire article can be read here:
AmericanHeritage.com / THE DEFENSE OF WAKE