A reasonable question might be asked of one who claims to be a naturalistic spiritual atheist and a witch...what purpose does the witch part serve? It would be just as easy to identify as the first part. So I feel I should say what I define a witch as, and why I feel affinity with the idea.
Witchcraft, of course, has many different meanings, depending on the source and context. The late Isaac Bonewits, a distinguished magical practitioner and Neopagan--the only one to ever receive a B.A. in Magic from an accredited university (UC Berkley) wrote an inimitable essay titled "Classifying Witchcraft" which breaks down many classifications of "witches".
Indeed, witchcraft can be historical or modern, real or fictional, secular or religious. A word that can mean anything actually means nothing, so if we are going to use it we should probably come up with an idea of what the common threads are.
The first and most obvious would be the practice of magic, conceived of as supernatural or natural. Many modern witches, when differentiating Wicca from witchcraft (a very common confusion) would point to this distinction. "Wicca is a religion, witchcraft is the practice of magic". But that definition is problematic as well.
After all, if my definition of magic stands, namely "symbolic action meant to facilitate the manifestation in the real world of the magician's intent" then it becomes clear that many people who would not call themselves witches are practicing magic. Intercessory prayer, so common among the Evangelicals with whom I grew up, could not be defined in any other way. People pray for a spiritual entity to intervene on their behalf in times of need (or simply desire). Those Evangelicals would be loathe to call themselves witches, and many self-identified witches would be equally loathe to accept them in our (their? the?) ranks. Another point of contention would be many ceremonial magicians (Kabalah, Golden Dawn, etc.) who would also consider it an insult to be referred to as a "witch".
So if magic is not sufficient for defining witchcraft, what is the distinguishing factor? Well, I have an idea. In all anthropological forms and modern manifestations, witchcraft seems to be the practice of magic in an unofficial spiritual framework. In general terms, most societies show a sharp divide between what is officially sanctioned and what actually happens on the ground on one level or another. The "official" language of a country may only be spoken by a minority of the population (i.e. English in Puerto Rico, French in Haiti) and the "informal (unofficial) economy" might be the primary economic sector! I think something similar happens to phenomena known as "witchcraft" in modern societies. Witchcraft is simply a reflection of the same official(artificial)/unofficial (real) dichotomy applied to magic. Witchcraft is unofficial spirituality,--bootleg magic.
Most African-Americans have historically been Protestant Christians. And yet, the practice of Hoodoo, folk magic, was quite common. Hoodoo doctors and rootworkers offered services to their communities, presumably in many cases to people who considered themselves Protestants and also went to church. Santería practitioners often provided their services in communities where people consider themselves Catholics. In the context of the United States, both served an oppressed population (African-Americans and Latinos respectively).
Socioeconomic status of practitioners is an important clue in this regard. In most cases, ceremonial magicians have deliberately distanced themselves from folk magic practitioners and aligned themselves with the dominant religion. The actual practitioners have tended to be people of privilege--male, white and highly-educated in many parts of Europe. They considered themselves an elite spiritual society, but still within the dominant spiritual power structures. A comparison between ceremonial magicians and witches might be akin to comparing a special forces unit and a vigilante group. Both are small groups that use force, but only the force of the first group is considered legitimate; force by the second group is not. If you want an example, a blogpost by Peregrin Wildoak on "Practical Magic" gives the view of one ceremonial magician on magical practice that many would call witchcraft.
Something interesting to note is that the more officially-sanctioned a magical practice is, the less likely it is to be called witchcraft. The most obvious example is the Christian Church, but take for example Wicca. As Wicca grows in official acceptance, with legally-recognized chaplains and churches, more and more Wiccans shy away from the title "witches" even though Gerald Gardener originally called the religion "witchcraft". If Wicca survives another hundred years, it would not surprise me if it nominally cut all ties with "witchcraft". (If you compare early Christianity with its modern varieties, you will realize that stranger things have happened.)
This is something alluded to by Miguel A. De la Torre in his book Santería: The Beliefs and Rituals of a Growing Religion in America. He denounces the fact that Santería is also referred to as "witchcraft" by many members of the mainstream religion.
"The French philosopher Pierre Bourdieu contends that 'sorcery' and 'magic' are names imposed upon the religions of those existing on the margins of society in order to disqualify them. Those who do this naming, of course, use the legitimating term 'religion' to refer to their own brand of sorcery and magic.2"
Indeed, magic seems to be like language. Just as the prestige of a language variety is only defined by the prestige of its users, the prestige of a magical system is defined by the prestige of its practitioners. Witchcraft is magical practice outside of the official and prestigious religious or spiritual power structures. This is not necessarily dependent on the use of "harmful", "baneful" or "black magic" by the practitioner in question. Reputed "good witches", or so-called benevolent low-magic practitioners such as the "cunning folk" in Britain were seen by the dominant religious authorities (albeit not by the local populations) to be in cohorts with the Devil, even though the community generally acknowledged them to be helpful.
Also like language, boundaries between the prestige and non-prestige varieties are enforced, but in an unequal way. The prestige variety always has more leeway to enter the space of the non-prestige variety. If a non-prestige variety is seen as encroaching on the territory of the prestige variety, then its users are seen as socially disruptive.
It is this transgressive aspect which defines witchcraft for me. A witch was not just a magical practitioner: she was an "uppity" woman. Witchcraft is magic + transgression. This transgression often takes the form of gender norms. I feel transgressive and adhere to the idea, but not out of a simple, adolescent-type desire to "rebel". My opinion is that it is often in transgression of categories, or even the combination of contradictory categories that higher truths can be found. In different points of my life, if people asked me if I believed in God, I would say "yes" or "no". Now I'm in the comfortable position of being able to say "both", or call out the person for asking me a leading question. The question of whether God exists depends on your definition of God; it is not at all a neutral, straightforward concept. Most people are so steeped in their cultural, pre-packaged definition of God, that they are blind to its influence. Stepping outside of that consideration is what allows for a greater truth to be understood.
Witches use what works in their magic, whatever symbols and available materials allow them to transcend their normal, expected social and personal limits. In my practice, I think that allows me a more integrated perspective of self, a greater sense of personal power, and a more enlightened view of the universe, which I still am quite far away from understanding. But every little bit helps, and that's what the "witch" label does for me.