The account of Clifford slaying the unfortunate Rutland in this fashion comes from one sixteenth-century source: Edward Hall's Union of the Two Noble and Illustre Famelies of Lancastre & Yorke:
While this battaill was in fightyng, a prieste called sir Robert Aspall, chappelain and schole master to the yong erle of Rutland ii. sonne to the aboue named duke of Yorke, scace of y age of. xii. yeres, a faire getlema, and a maydenlike person, perceiuyng y flight was more sanegard, then tariyng, bothe for him and his master, secretly conueyed therle out of y felde, by the lord Cliffordes bande, toward the towne, but or he coulde enter into a house, he was by the sayd lord Clifford espied, folowed, and taken, and by reson of his apparell, demaunded what he was. The yog gentelman dismaied, had not a word to speake, but kneled on his knees imploryng mercy, and desiryng grace, both with holding vp his hades and making dolorous countinance, for his speache was gone for feare. Saue him saycle his Chappelein, for he is a princes sonne, and peraduenture may do you good hereafter. With that word, the lord Clifford marked him and sayde: by Gods blode, thy father slew myne, and so wil I do the and all thy kyn, and with that woord, stacke the erle to y hart with his dagger, and bad his Chappeleyn bere the erles mother & brother worde what he had done, and sayde. . . . Yet this cruell Clifforde, deadly bloudsupper not content with this homicyde, or chyldkillyng, came to y place wher the dead corps of the duke of Yorke lay, and caused his head to be stryken of, and set on it a croune of paper, & so fixed it on a pole, & presented it to the Quene, not lyeng farre from the felde, in great despite, and much derision, saiyng: Madame, your warre is done, here is your kinges raunsome, at which present, was much ioy, and great reioysing . . .
There are several problems with this account, however. First, Rutland was not barely twelve, as Hall depicts him, but seventeen. As such, he was fully old enough to be fighting, just as seventeen-year-old Edward of Lancaster, Prince of Wales, was old enough to be fighting at Tewkesbury eleven years later. And just as both young men were old enough to fight, they were also old enough (by the standards of their day) to die. (Edward the Black Prince, it should be remembered, put his life at risk fighting at Crécy when he was just sixteen.) Killing Rutland at Wakefield in 1460 was no more a child-killing than was killing Edward of Lancaster at Tewkesbury in 1471.
Second, Rutland's age is not the only thing in Hall's account to be demonstrably muddled: though Hall depicts Margaret of Anjou as "not lyeing faree from the felde," she was in fact some distance away, in Scotland. (The story of York being given a paper crown, however, does appear in the Annales Rerum Anglicarum, though neither Clifford nor Margaret is mentioned as being involved in the "crowning.")
Third, no contemporary account of Wakefield relates this pathetic scene, or anything like it. Gregory, who describes Rutland not as a maidenlike person but as "one of the best disposed lords in this land," simply mentions him as being taken and slain. A newsletter dated January 9, 1461, reports of the battle, "Ultimately, they routed them, slaying the duke and his younger son the earl of Rutland, Warwick's father, and many others." The Crowland chronicler in his brief summary of the battle of Wakefield does not even mention Rutland's death. The English Chronicle states, "When they saw a convenient time to fulfil their cruel intentions, on the last day of December, they fell upon Duke Richard, and killed him, his son the Earl of Rutland, and many other knights and squires." The Annales Rerum Anglicarum states, without further elaboration, "And in the flight after the battle, Lord Clifford killed Edmund Earl of Rutland, son of the Duke of York, on the bridge at Wakefield." None of these sources are friendly to the Lancastrian cause or to Queen Margaret, and some are downright hostile; had there been a horrendous story connected with Rutland's death, it's reasonable to think they would have mentioned it.
Clifford himself was killed in battle on March 28, 1461, the day before the battle of Towton. Like a host of other Lancastrians, he was attainted by Edward IV's first Parliament, which met that November. Notably, although the roll for this Parliament refers to the "murders" of the Duke of York, the Earl of Salisbury, and the Earl of Rutland and deplores the beheading of the dead bodies, it does not distinguish Edmund's death as being more horrid than that of his elders:
Wheruppon, at Wakefeld in the shire of York, the seid duc of Somerset falsely and traiterously the same noble prynce duc of York, on Teuisday the .xxx. day of Decembre last passed, horribly, cruelly, and tyrannyously murdred; and also the worthy and good lordes Edmund erle of Ruthland, brother of oure seid soverayne lord, and Richard erle of Salesbury; and not therwith content, of their insaciable malice, after that they were dede, made theym to be heded with abhomynable cruelte and horrible despite, ayenst all humanite and nature of nobles.
Besides Hall, another sixteenth-century source, Leland's Itinerary, does mention Rutland's death. Significantly, though Leland claims that Clifford was known as "the Butcher" because of his part in the battle, he does not connect this epithet with Rutland's death in particular:
There was a sore Batell faught in the south Feeldes by this Bridge. And yn the flite of the Duke of Yorkes Parte, other the Duke hymself, or his Sun therle of Ruthelana, was slayne a litle above the Barres beyond the Bridge going up into the Toune of Wakefeld that standith ful fairely apon a clyving Ground. At this Place is set up a Crosse in rei memoriam. The commune saying is there, that the Erie wold have taken ther a poore Woman's House for socour, and she for fere shet the Dore and strait the Erie was killid. The Lord Clifford for killing of Men at this Batail was caullid the Boucher.
If Clifford did indeed kill Rutland, as stated by Annales Rerum Anglicarum, it's quite plausible that he relished doing so: his father had been killed by York's forces at the first battle of St. Albans, and he and the heirs to the other lords who had died there were notoriously eager for revenge. And Edmund's death at seventeen was undeniably a tragedy, as is the death of any young person. But unless one credits Hall's entire story, which is demonstrably inaccurate in spots and which in its details of Rutland's death is not corroborated by contemporary accounts except in the particular of Clifford being Rutland's killer, there is no reason to regard Rutland's death as a war atrocity.
Keith Dockray, Henry VI, Margaret of Anjou and the Wars of the Roses: A Source Book.
Henry Summerson, ‘Clifford, John, ninth Baron Clifford (1435–1461)’, Oxford Dictionary of National Biography, Oxford University Press, Sept 2004; online edn, Jan 2008 [http://www.oxforddnb.com/view/article/5654, accessed 17 Feb 2010]