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Most branches of Christianity has always associated witchcraft with the devil, or some form of demon worship. This has been used as an excuse for the persecution of innocent people who were seen as threats to society. (The Salem trials, the Knights templar, etc.).

What I want is for the Catholic Church to embrace witchcraft as a legitimate craft in the dark ages, and frame it as a tool for good. However, for whatever reason, only women have the ability to perform it. This is a problem as it can be seen as a challenge by officials to the role of men as leaders.

How can the church incorporate the practice of witchcraft into its practices without changing the status quo?

How exactly are you defining witchcraft? It’s a tricky one, but aligning witchcraft with midwifery might get you somewhere with “only women have the ability to perform it”. I’ll have to come back to edit this, but I think Diane Purkiss has done some good work looking at the overlap between late medieval midwifery and witchcraft - if the Church sanctioned midwifery, encouraged the use of birth girdles and other ‘superstitious’ items, and allowed charms and amulets (have a look at Don Skemer’s book on Textual Amulets), then the two might have gone together without the negative connotations that actually ended up happening.

The other things worth looking at are accounts of mystical happenings. Again, I’ll come back and edit this when I’ve got all my notes, but there are examples of things like mystical pregnancies (generally women swelling with the Holy Ghost), devotional anorexia/inedia (surviving solely on the Eucharist), and other things that generally happened to women. Caroline Walker Bynum’s Holy Feast And Holy Fast is a great place to start if you’re interested in that kind of thing.

If you start with the kinds of things that were sanctioned (or even venerated) by the Catholic Church in the period you’re interested in, especially things that happened to women specifically, then use that as a basis from which to build your witchcraft practices. Female healers? They could be church sanctioned midwives. Able to perform miraculous acts? Incorporate them into hagiographical tradition. :)

Actually, Catholic doctrine didn't include belief in witchcraft most of the time. To believe that simple village women would make deal with the devil and gain thereby magic powers was a heresy of itself.

The Germanic Council of Paderborn in 785 explicitly outlawed the very belief in witches... (from Wikipedia)

Even the 'Hammer of Witches', although written by Catholic monks, didn't find much popularity among Catholics, and was more popular among Protestants.

It wouldn't, however, make witchcraft any more palatable for the Church on itself. I think, the easiest way to make medieval clergy tolerate magic of any kind would be to treat it as science, as a result of manipulating natural laws in any way, rather then as any mystical process.

Another possible variant, although more problematic in my opinion, would be to treat magic as a result of prayer, a miracle. If your witches would use the trappings of Christianity, pray to the God and St. Mary, use crucifix as a ritual tool, possibly, maybe, it could be seen as a miracle granted by the God. That the women were able to do that, and not men, could be seen as a special intervention of St. Mary for the other womenfolk.

The second version seems to be a bit more problematic to me, though. Magic as science would be no different from medicine, while magic as prayer would be in conflict with Church hierarchy. It would mean more conflicts and power plays inside the structure of the Church. Special monastic orders of magic-women, maybe, the attempt to keep them from high positions in the Church by men. It would be complicated.

How to incorporate magic? Very easily. Slap a Saints name on it.

https://www.catholic.org/saints/stindex.php

https://en.wikipedia.org/wiki/List_of_saints

If there's not a saint for what you want, call it a Jesus something or another.

How to integrate woman controlled powers? A few different ways, but totally still doable.

Chain them to a controller that's male. It would require a cradle to grave scheme, trained from birth. Sequester them to nunnery. How do humans control other humans? Lots of ways.

Women have always had a place in the Catholic church. Any religion involves some magic.

Step one: find some heathens and learn their culture.

Step two: take not of whatever parallels you can find between their heathen culture and your own. For example, if they believe in a master god, you can trace a parallel to your own single god.

Step three: copy their traditions, but replace all the symbolism with sigils and images from your own tradition.

Step four: repeat all steps above, ad infinitum.

For example, the Bible says that Jesus was born around the time of a heathen census, and those did not happen in December. But some heathens that the church really wanted to convert only celebrated their major god birth on the solstice of winter, so the church preached to them that it was JC's b-day that was actually being celebrated that time of the year. It stuck, and to this day we celebrate the day when the three wise men (or twelve, depending on tradition) dressed in red and broke into the stable where Mary gave birth through a chimney to put some incense, gold and... stuff into his socks.

There was also something about a mesopothamian goddess of fertility that was celebrated some moons after the other heathens orgies. But you know how these kinds of things always get lost through the ages and translation, so now we celebrate the rebirth of god by evoking a bunny which lays colored eggs (in some countries, those eggs are also made of chocolate).

Sometimes you get a twist when you try to reform your own religion. One person's celebration of the time when their people escaped slavery by running away from it is someone else's celebration of someone being flogged and hanged on a cross in a very passionate manner.

Last but not least, about only women being able to do it: if you are running a machist, mysoginistic organization in a world where women can evoke fireballs and hurl them at you, it is in your interest that they are no longer able to cast magic and that all the knowledge on such things is controlled by the patriarchy. Because the moment they learn to cast again, the evil system goes down. This is actually why the priests are forbidden from marrying and stuff.

There is some debate on the Old Testament translations from Hebrew into Latin and English around the topic of witches and wizards. The term poisoner is thought to be more accurate than the Witch or Wizard. Some people, in modern times, have used that fact as fodder for the arguments that the prohibitions on witchcraft were actually male chauvinism seeking to control the practice of midwifery.

But, in the context of when the Hebrew Bible was written, it is thought to have meant people that use witchcraft to harm another.

If this idea is acceptable, then your story's Catholic World might accept witchcraft if it was used for good purposes and not selfish purposes or injuring another person. There are still many prohibitions in the Bible against interacting with familiar spirits and demons, so the rest would be how does witchcraft work in your world.