Yes, the stereotype you describe is a wonderful tragic figure for modern readers--immediately sympathetic. A woman, well-connected and well-liked in her community, shut out of the formal academic medical realm and still making her own way, independent even of a husband. She practices a form of science in her own right, and it's those superstitious religious authorities who scorn alternative medicine and uppity women. This figure is an interesting development from the previous, perhaps more common outside of fiction stereotype of the witch as the female outcast.

The history of witchcraft in medieval/early modern Europe is a story of exceptions, not rules, and as your question already indicated, the key here is looking at "various parts of the stereotype."

Broadly speaking, we can talk about two basic types of witch accusation: individual accusations usually leveled by one or more members of a community against another; and outbreaks of many accusations that seem to take on a life of their own, propelled onward by community members piling and/or inquisitors torturing witches until they named everyone they could think of as another witch.

In the second situation, pretty much anyone could be up for grabs. In rural Franconia, accusations frequently targeted a male patriarch and then all the women in his family. Johannes Junius of Bamberg recounted (in a letter smuggled out of prison to his daughter) how the inquisitors would name a street in the town, torture him until he named "enough" people who lived on that street as witches as well--and then move on to the next street. Outbreaks cease to be about the individual. Well, mostly.

As I mentioned in the AMA, inquisitors in outbreaks did have and exercise a choice as to which denunciations under torture or threat of torture they pursued. J.B. Durrant did indeed find that in Eichstatt, inquisitors followed up denunciations of female witches far, far more often than men. But here is where the stereotype starts to break down. Anna Harding is the female professional healer caught up in the Eichstatt outbreak. Apparently she was the town's go-to woman if your period stopped and you needed it to start again (read: providing abortifacient herbs). Harding was married (good); she was a prostitute (bad); her ecclesiastical interrogators did not seem to care at all about her sexual transgressions (what?). The fascinating thing about Harding's case, however, is that her uses of herbal medicine did not implicate her as a witch. While the inquisitors asked her if her ointments included diabolical incantations, she denied it. In the end, Harding was convicted of witchcraft to inflict harm...against her own livestock.

In cases of isolated accusations or small clusters of accusations, there is more room for the individual to matter--though frequently within some kind of local pattern. For example, Rune Blix Hagen points out that in western northern Norway, the majority of witch accusations come against men--especially of the Sami people--who used drums as part of their prayer practices, evoking the concern of religious authorities. In the eastern north, specifically along the coast, accusations targeted women viewed as rebellious in some way (not related to presumed magic in the same way as the Sami men--girls younger than 12 were accused and even executed).

The specific connection to herbs and healing in the stereotype does reflect modern ideals of rationality if we are meant to sympathize with our fictional persecuted witch, but it's a very uncreative interpretation of the extent of medieval magic. Here we have to distinguish first of all between "private" and "public" magic/magic-tinted acts, or the little things many--most?--people did for themselves and their families, and the magical acts that people performed as a service to others, likely for pay. (Like women in labor holding onto charms of St. Margaret or a piece of paper with some words from her hagiography as a ward against death in childbirth). But more to the point is the immense diversity of magic in late medieval Europe!

Why stop at healing? Treasure hunting, love potions, fortune telling...it's all there; it's all magical. By the late Middle Ages (earlier is perhaps questionable--have we got a historian of Anglo-Saxon medical texts here?), people understood the difference between "administering an herb" and "administering an herb plus saying an incantation over it and lighting candles that you walk around four times." On the other hand, we know from accusations of treasure hunting that authorities often suspected that if the non-magical behavior (digging; herbing) was evident, surely there must be incantation and magical ritual.

Some public practitioners of magic specialized; some didn't. This is a confusing situation because someone like Maria da Vicenza could be described as "medica", yet the accusations against her seem rooted in love spells and potions. Indeed, witches in Italy--mainly female--are most typically linked with love magic rather than healing. One Bolognese woman was convicted of curing people with herbs after causing harm to them magically, in order to profit. That case probably gives insight into the mental processes of some of the accusations of "cunning folk"--where there's a cure for money, there was harm first of all. But we can't have everything; our Bolognese herbalist was the wife of the city notary himself!

While many witches like the unfortunate notary's wife were executed, particularly in cases linked to "benevolent" public magic, that was hardly the rule. There's a great case of magical treasure hunting in Augsburg where the punishments of its participants ranged from exile from the city to a week in jail to "being given a good talking to." Raisa Maria Toivo's case studies of Finland turned up a woman who fits some of the stereotype that we haven't yet seen: a widow, older, quite craftily managing to hold onto some of her late husband's estate for her daughter, quarreling frequently with neighbors--who ends up accused and even convicted of witchcraft multiple times, only paying a fine each time. It seems to be the case that executions were rarer in the Nordic countries overall, though Hagen observes that witchcraft was the most prevalent crime among people executed by far in his studied territories. (I've also read that executions were less frequent in Italy overall, but then basically all the individual case studies I've read end in death, so. Well, in one case local boys rescued the convicted necromancer--a priest, talk about defying the stereotype--from the pyre. But still.)

As to defying the religious authorities...this is perhaps the most contested and most complex situation. Witchcraft can be both a secular and religious crime, but to different degrees in different places. In Italy, witchcraft is heresy and pursued by the inquisition. In Denmark, it's a secular crime. In other places, it's complicated. The role of local communities versus civic/religious officials in fomenting outbreaks and even triggering individual accusations is hotly debated, even on the basis of the same evidence.

Jordana de Baulmes' case shows us just one way the evidence can be controversial. When she was called before the inquisitors of Lausanne, she remembered a neighbor telling her that he believed she had caused his livestock to die, and he would see her burn for it. So we have evidence of a prior accusation. But then the inquisitors would not let go. She even confessed to attempted infanticide (the child had died, but, she stressed, after a last-minute baptism)--the worst crime a woman could commit in medieval Germany, subject to the most brutal form of execution--and still the inquisitors wanted their witch confession. At one point they interrupted the interrogation process to let her sit in jail for seven weeks. Is this a case of community or authorities driving the process? Who is responsible for driving forward the ideas about witchcraft? Richard Kieckhefer has shown that diverse local ideas of the witch eventually streamlined. (There are always some regional differences, but...witch confessions are remarkably similar over western Europe.)

So basically, all the individual parts of the "independent woman healer versus the inquisition" were present in the medieval/early modern witch panic. They coalesced into one person to varying degrees in different times and different places, and sometimes none of them were present. Most witches (75-80%) were female. Most cases involved religious authorities to some degree, sometimes a very very great degree. Some cases involved a public practitioner of some form of magic--not always healing with incantations, and typically a magic tinged with Christianity. (For example, invocations of the Virgin Mary in treasure hunting or magically learning to read overnight). Witches frequently had strong social ties, although not always positive ones. They ranged the socio-economic scale. And sometimes, absolutely nothing else mattered except that another witch being tortured had met them that one time and pulled out any name at all to stop the pain.

I'm sorry this is such a deeply unsatisfying "answer."