Each idea, requires either adding soem flexibility on church's ideas, or stretching the definition, usage and limits of witchcraft.
Idea 1: "We live in darkness to serve the light."
Okay, very basically, witchcraft in medievel fantasy settigns can do some nasty stuff, depends on definition. But being usually associated with demonic powers, witchcraft is known to inflict misery.
But, power is power. There was a historical example I vaguely remember about a pope, claiming he had literal demons chained under the church's basement.
Think of something like that. An enslaved demon, and church is using that demon's powers with the help of many women who can channel that power.
"They reminds us what the dark powers can do, they offer us a way to undertand and build counter-measures against it, and they offer us a wide arsenal of powers in our command. A... Necessary evil."
Idea 2: "Our curse is our blessing."
Maybe witchcraft is originated from a curse. Or takes a heavy toll. So, only a special group of women, who can handle the side effects, and specially trained, indoctrinated, are serving to the church as assistance in areas where non-magical methods won't work. But all actions of these women needs to be regulated.
That is why "wild" or "rogue" witches, who perform witchcraft outside church's interference, are known as heretics and dangers. So they are executed on the spot. Some other women can also wield and learn witchcraft, but it is not systematic.
Idea 3: "Monster on leash"
Inquisitors aided with trained, perhaps tortured witches. Maybe they were broken by other means. Up to you. Church takes and raises whoever they can control, and kills those who they can't control. All for the sake of power, all because of the arrogance of the bishops and pope himself.
Idea 4: "These nuns are too good of a fighter/healer/scholar for a human!"
Witchcraft, is not exactly openly performed, but rather, a group of nuns who wields weapons and trained in martial arts or trained in healing etc are actually performing witchraft to further boost their abilities. But, they are a seperate organization under the church who plan on their idea of devotion by whatever means necessary. So, for others, they are just "Nuns who are exceptionally trained." And they become a nun to hide their methods under the church's protection.
Idea 5: "Weapons of my enemies."
Maybe women can "activate" artifacts made by witches, and they can use these "artifacts to full potential because females in this setting has a naturally higher magical or witchcraft talent. And it shows.
So, these women can "use" witchcraft based tools and methods, but are not witches themselves. All these artifacts were actually creation of witches church took. And someone figured out that women can use these artifact. Creating a defence force who can actually benefit from the "weapons of church's enemies."
Idea 6: Desperation
Maybe the famine, plague, wars and many other disasters you could add, caused the church and people following them to be desperate. So, they captured young witche trained them, and added them to their ranks. It was not something church planned, or even wanted. But, desperate times brings desperate measures.
Idea 7: Puppet or battery
Maybe the "burnt" witches are not actually burned, but taken to a special place, placed under a... surgery... that deprived their senses, and allowed someone to wield them as staffs or sources of magic.
Maybe these witches were turned into small containers that grants power of witchcraft to whoever female, touches it. Maybe church is using these "witches" as battery for magic and training lots of women just to use all the witches they captured and... turned.
Check out the catridge of the bondrewd from made in abyss. Similar method.