"What little I have discovered points to the witches of Glenmoril. In the past, they have been capable of creating a cure. I have searched for these witches throughout Cyrodiil, but no covens still exist within its borders. There may be one left. I have unconfirmed reports of a woman seen near the Corbolo river, who fits the description of these witches"-Janus Hassildor.
http://www.uesp.net/wiki/Lore:Vampires_of_Vvardenfell#Volume_II
"In the West, a shadowy fraternity of vampire hunters is believed to be primarily composed of formerly afflicted vampires who have been cured of the disease. According to legend, the Vampire Hunters refuse to reveal the cure to the disease for fear that it may encourage depraved thrill seekers from deliberately infecting themselves."
http://www.uesp.net/wiki/Lore:Vampires_of_the_Iliac_Bay
"There are several of us, you see, former vampires who know what to look for. We're patient too: we learned it in our unlife. We watch and listen, and anonymously contact the vampires we know wish to end the curse. Ending the curse is possible, but only just. It is very dangerous, but when you are cursed, the only real danger is no escape."
Now, why would vampires in Cyrodiil be responsible for the deaths or the lack of Witches in Cyrodiil? Because the fact that they can cure vampirism, and the book, "Vampires of Vvardenfell" states that those cured vampires seek to destroy their former brethren. Since the cure was obviously retrieved from the Witches, since they are the ones always able to cure it(Aside from the Daedric Prince or killing the bloodfather as stated on Daggerfall). Now, what do we know of the Cyrodiilic vampire clan?
http://www.uesp.net/wiki/Lore:Immortal_Blood
"I told him what I could. There was but one tribe in Cyrodiil, a powerful clan who had ousted all other competitors, much like the Imperials themselves had done. Their true name was unknown, lost in history, but they were experts at concealment. If they kept themselves well-fed, they were indistinguishable from living persons. They were cultured, more civilized than the vampires of the provinces, preferring to feed on victims while they were asleep, unaware."
From this sentance alone we can see that these vampires dont take crap from no one, since they are the ONLY clan in Cyrodiil means they wont accept other competitors in their border and they dont like to share, menaing they are very power hungry indeed. Now, take a look at this.
http://www.uesp.net/wiki/Lore:Manifesto_Cyrodiil_Vampyrum
"On Our Order:
Know first that we are no simple tribe of savages, tearing throats with the orgiastic abandon of our scattered, tribal brethren. Ours is a civil fraternity, to which we are bound - every one - by our dual hunger for flesh and influence. By the virtue of Imperial structure and bureaucracy, Cyrodiil has become our stronghold in the third era, and we suffer no savage rivals within our boundries, reveal ourselves to none, and manipulate the hand of society to mete out our agendas."
"On Our Rivals:
Most barbaric tribes think themselves powerful by the gift of Bals blood alone, and squander the gift. There are those, however,who show signs of enlightenments, and earn our attention - those such as Glenmoril Wyrd, who live within the walls of Breton cities, or the Whet-Fang sodality of Black Marsh, who use magicka to keep captives catatonic and harvest from them the red nectar. These foes may one day threaten to impugn our sovereignty within the boundries of Cyrodiil, thus compelling our vigilance. Should and enroach upon our dominion, our wrath must be swift and total."
Right there, clearly states that the Witches are indeed enemies, although respected by the Order, they are still enemies that will incur the "Wrath" that will be "Swift and total" from the Cyrodiilic vampires. How will they do it? Either manipulate someone to kill them off or do it themselves, since they are to "Manipulate the hand of society" and "Reveal ourselves to no one"
A good example of this is Janus Hassildor, a possible member of the Order, he is civilized, lives in Cyrodiil and disguises his appearance while remaining incognito from mankind. Other members can be recorded also, such as Jakben Earl of Imbel, who masquerades as a nobleman in the Imperial City. Seridur, obviously sends his men to kill vampires while he himself is one in disguise. And Lord Lovidicus, father of Agronak-Gro Malog, who is a nobleman with a dark secret(Hes a vampire), who also broke the core tenet of the Cyrodiilic vampire clan "Above all, reveal thyself and our Order to no other, for discretion is the greatest of our virtues."
"I assure you, I am not responsible for them. I would never be so careless. Where there are mindless animals, predators are never far behind. This is not the first time such a thing has happened, however. On some level, they’re aware of my presence. Whether they covet all that I have, or simply wish to see it destroyed, I do not know. They have given in to their instincts, and are little more than animals. They need to be exterminated, one way or another." Janus Hassildor on the vampires of Bloodcrust cavern.
That shows that he hates those barbaric animalistic vampires, mentioned in the book, "Manifesto Cyrodiil vampyrum", which states that they must kill off barbaric rivals in the border.
Also, take a note of this: On the topic of Bloodcrust Cavern he will simply say: "The Cavern is silent once more. I would be foolish to think that this might send a message to those who would encroach on my territory.
Now, why would Cyrodiilic vampires have a need to kill off the witches? And why is Melisande alive? And how does Janus Hassildor know of her?
1. Because "Vampires of Vvardenfell" stated some former vampires who were cured, began hunting down their former vampiric brethren, explains why the Vampires of Cyrodiil needed to end the source of the cure, so no one could cure themselves and begin an idealistic crusade against the Order, bcause the worst enemy besides outsiders can be the one from inside, who knows everything and will reveal everything, which would be a major danger for them.
2. Melisande lives still, but why wasn't she killed off? Because Melisande "Gave up witchcraft years ago", which deemed her someone who is no longer a threat. But that didn't stop her from forging a cure for the Count and the player, did it?
3. SInce Janus is always hiding behind his room, how does he know that there is still a witch there? Because he might be of the Order? or one of his informants told him. But being a vampire, means he has veyr few allies.
Just a speculation, haha.