Does the fact that the Rot solely affects creatures the sheep hate not imply that it is sapient?
Yngya tells Lamb that they are immune to the Rot (implied when she tells them not to fear it).
Hagar is only Rotten during her boss fight, it powers her, but she is freed once she's defeated. The Woolhaven flock despising Hagar doesn't negate the fact she dedicated her remaining life to tending to the sheep graves, punishing herself, and later serving Lamb. The Woolhaven flock do not speak for all sheep and their opinions of Hagar.
Fox can eat Rotten followers without getting sick. Helob says the Rot followers aren't good for eating which implies that he too has tried one before.
Gofernon doesn't get sick despite frequenting Ewefall AND the Rot via tunneling.
But Thoas and Gorgo stay Rotted as followers and aren't eligible to be cured? The wolfdog brothers immediately swear themselves to Lamb and are completely unRotten after indoctrination.
Yet, Thistle is diseased and murdered. Marchosias is diseased, alongside the majority of her Pack. I don't know what animal Thistle is, but if it's true that despite looking like dogs all the minibosses are wolves? That means the Rot especially targets wolves and fucking kills them. How can you explain away the inconsistencies of this disease? It spreads through bodily fluids (confirmed through the mating tent aspect of one Rotten follower and one normal follower resulting in two Rotten followers and a Rotten egg). So?
Also applies to Ophans and Eleleth, two sheep. Eleleth maintains a red/Rotten face even after being cured. Ophans has a red/Rotten body with matching wool. In the Rot, Eleleth is characterized as wearing a two-faced sheep mask, hiding their body with a cloak, and carries a knife behind their back. Their corresponding Flockade piece is named Lornlileth, Rotten Sword, and they're heralded as the one who murdered Tooth and Claw.
In the Rot, Ophans has a chained face, an Old Faith robe, a Crown of Thorns like headpiece, and wears a cage full of Rotten creatures on his back. Ophans's design implies that while alive, she was a follower of the Bishops who most likely aided them in capturing and killing other sheep. The minor enemies that resemble him use the same chained scythe weapon, except theirs has a Rotten sheep attached. Ophans's corresponding Flockade piece is named Antons, Rotten Scribe, and is said to have been a decipherer of ancient scrolls and tombs.
These two (alongside Poyel but I am still working on a theory for their betrayal and demise) are visually marked by the signs of a traitor. Two-faced, dagger, cage of fellow sheep, and the garb of those who ordered the genocide of all sheep to begin with are all indications for what their roles are meant to be.
Poyel can also be mentioned, as he also has a Flockade piece named after himself. Elyon, Rotten Shield, known as the Hero of the Grasslands. Their Rotten form walks on six legs, has no face, and is riddled with holes. Being cured leaves Poyel without horns, ears, wool, and with several holes still gouged into his head. The Rot being full of sheep themed iron maidens, alongside the decor piece titled Iron Maiden of Ram Horn (description: even the peaceful may be pushed), has led me to believe that Poyel was murdered by other sheep for a perceived or real betrayal. I think multiple weapons were used but the canon one was most likely the iron maiden.