It has been said that the dead need to be given due respect, but exceptions are generally made for traitors. And the higher the one performing the treachery, the more disrespect that can be done that doesn't seem inappropriate for the situation. For Princess Celestia dealing with "Mr. Hoofer", a high amount of disrespect to his body was acceptable, but she would not give it herself.
For him, she authorized an old and relatively cruel punishment: public burning at the stake. His dead form would be tied to a large pole in the middle of the plaza in front of the palace, and the pole set aflame by a blast of Celestia's own magic. This punishment once was a metaphorical representation of "the sun" (i.e. Celestia herself) consuming those who would turn against her. Curiosity about the old style of execution and the relative high profile of the traitor being burned at the stake would ensure a high turnout for the event and extensive media coverage of both it and the aftereffects. It was as much about making a statement as it was in serving justice for those who "Mr. Hoofer's" actions lead to being killed or injured, or so it was believed...
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The view of the spectacle from the castle windows was both morbidly curious and morbidly scary. This unease was compounded by the revelation that the EIA had more Agents of Chaos in its ranks than just "Mr. Hoofer" - in fact, as documentation seized in the Fidelitas-led raid began to be sorted through, there was every indication that those members in the EIA were used to help cover the actions of others.
It was the implications of the seized documentation that made Captain of the Guard Gibraltar depressed as he sorted through the preliminary report of the raid on the EIA headquarters. Most of the report was a detail of the actions taken and the brief fight outside the building gate, but also buried inside was a list of the identities of Agents of Chaos within the EIA. All intelligence given by them to Gibraltar or the princesses directly was now suspect, and Gibraltar had the sad task of disposing of all suspect intelligence reports - most could not be verified by other sources to check their authenticity.
As Gibraltar was moving through the paperwork, he noticed a small note stapled along the edge of one of the pages. The note showed signs of being scrawled in a hurry and probably by a non-unicorn member of the Guard - the writing would not have been of acceptable quality for unicorn members - and then attached to a seemingly random page in the middle of the paperwork stack. It was a reasonably good way to get a secret message passed along in a hurry, so Gibraltar stopped his other work to try to decipher the note.
The words were simple, but extremely alarming: "Inconsistencies between claimed attacker description and actual pony description discovered - magic color different. Leader may still be alive and loose. - Double Bar"
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Gibraltar knew who "Double Bar" was - it was his double agent within the Agents of Chaos that had helped thwart several of their plots. The fact that he was saying now that "Mr. Hoofer", who was currently under the process of being publicly degraded by an angry crowd, wasn't who everypony thought he was extremely alarming, as "Double Bar" was now the only trustworthy intelligence source Gibraltar had for determining what the Agents of Chaos were up to.
He took a look out of the office window at the crowds in the plaza - clamoring and throwing objects at the outstretched dead form of "Mr. Hoofer", all the while eagerly anticipating watching him burn. He wondered what was happening to Equestria, whether Luna's return and the rediscovery of the Elements of Harmony had really been a good thing or just unleashed more deep seated problems between the different pony races. But most of all, he wondered whether the Agents of Chaos would make "Mr. Hoofer" a martyr for their cause instead of a dirty coward, to rally even more extreme elements to their ranks.
"Oh Element Bearers, I hope we will not need you to fight for harmony here in this city..." Gibraltar mutters out in an almost prayerful manner...
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A LITTLE LATER...
Agent Snake knew from the mighty roar penetrating even the mountainside into the caverns within that the bonfire consuming "Mr. Hoofer" had been lit. Although he couldn't see it himself for security reasons, the mental picture was delicious enough - the colorful crowd of Canterlot citizens jubilantly watching who they believed public enemy #1 burning on a pole, the downcast and somber Princess Celestia, the concern and worry on members of the Royal Guard, and most of all the fears that would certainly be stoked once the last ashes of the bonfire had been extinguished.
"Isn't it delicious, Agent X? And it's all thanks to you!" Agent Snake says as he turns to look at the pony beside him, which wears the same face and form as the pony burning at the stake outside the caverns, in the palace square.
Agent X gives a grunt nod of affirmation and gives two good stamps of the forehooves - a sign of particular satisfaction with the job he had just performed. By the time the loyal members of the Royal Guard had realized that they had been carefully misled by the actions of Agent X in disguise, it would be too late to mitigate its effects. Yes, several Agents of Chaos had been lost, but the leaky EIA had been sealed, and now the loyalists were essentially fighting blind and deaf with all other intelligence leaks sealed as well.
"They believe we are defeated and will let their guard down. We will storm through them when we get the sign - the sign of the pegasus ascendancy. In that moment all our hopes and dreams will be fulfilled. And what a glorious day that will be, Agent X!" Snake exclaims.
Agent Snake listened to the low rumble coming from outside with an eagerly evil grin, and X licking lips eagerly, almost as if it was a tasty meal he was eating. Both knew what that low rumble meant - a mob barely under control, and angry elements within it that could be utilized for the purposes of chaos. None of the Equestrian loyalists knew it, but the conditions of Operation Whirlwind were now step up, and it would only be a matter of time before it was unleashed upon an unsuspecting Canterlot population...