My guess, and it is just a guess, is that it would be country folk, poorly educated (if at all), and less under the immediate supervision of the Church than city-dwellers would be, who carried on a lot of the ancestral customs (just not what particular customs they carried on, or how they carried them on). And I think the customs would have been offensive to the Church, especially to the Church hierarchy. The Church just wasn't able to stamp them out in remote rural areas.
Probably there would have been a village Catholic priest, but he probably came from the same background as his parishioners and was hardly better educated than them, maybe with barely enough Latin to celebrate Mass (no Jesuit universities to train educated priests in them days). In the 16th century one of the complaints of the Reformers was the ignorance of the country clergy.
And of course, along with the village priest, there would have been a village wise woman. I guess--again, just a guess--she might have known more lore passed down from the ancestors than just the use of herbs, etc., to treat sick people and sick livestock.
I am certain of what I wrote about the complaints of the Reformers concerning ignorant clergy (at least in England, but I doubt it would have much different on the Continent). The rest--my guessing--may be rooted in vague memories of books read in college and graduate school. I still have in my library a book called Religion and the Decline of Magic, by Keith Thomas, which I read in grad school. I haven't looked into that book in years, but maybe some of what I'm guessing above is rooted in memories of Thomas.
Your guesses seem very plausible to me. Is
Religion and the Decline of Magic good? Sounds interesting.
Your account is similar to what I've found, Jeff. The early 1500s were actually part of the Middle Ages when there was much superstition and infighting among the religious sects. In Scotland, for instance, the catholic Mary, Queen of Scots, made witchcraft illegal in 1563, punishable by burning at the stake. So, if the old Samhain rituals were still practiced, it must have been way out in the middle of nowhere.
In fact, the more I read about it, the more Scottish magic and its practitioners seem to have had similar experiences as those growing up gay in 1960s Wyoming. 
More details here: http://skyelander.orgfree.com/witch1.html
I interviewed a Minneapolis author who wrote
Daughters of the Witching Hill, a novel based on a true story of a mass witch execution in about 1600 in a town in England where the book's author, Mary Sharratt, lived for a while. Apparently the case was well known in the area -- they used their witchy past as a tourist attraction much the way Salem, Mass., does. Sharratt did a huge amount of research on the case -- read the primary sources like handwritten court documents, took history classes at the local college, etc.
In this book, it's a poor older woman and some of her friends and family who were executed. And by poor, I mean they had to beg for whatever food they would eat that day. So poverty was one risk factor for being accused of witchcraft. So was annoying or angering an authority with power (which this woman had done). As was having been around anyone who got sick and died or lost a cow or whatever -- and in them days, as you can imagine, situations like that were hard to avoid. So it didn't take much. I've also heard that older women who
did have wealth were sometimes accused so the authorities could seize the possessions (much like now, when cops seize property of people who've been charged with, but not convicted, of a crime). I was surprised that, in this novel, the accused witch herself semi-suspected she was a witch. I asked the author about that. She explained that the woman would have believed the superstitions as much as the other townsfolk did. Why wouldn't she?
Anyway, to bring this conversation semi back on topic, the episode took place at the time of much religious shifting and upheaval in Europe. The old woman recalled the merrier days of her own childhood, when Catholics were in power. Now Protestants had taken over, and not only was life for ordinary people less carefree and fun, but monks and priests were hunted and executed to the point that they had to hide in people's attics the way European Jews did in the Holocaust.
And to bring it back almost completely on topic, I don't know how much Samhain is directly related to witches. I mean, certainly Wiccans today celebrate it. And maybe the wise women/healer types who served those small communities -- and might have been accused of witchcraft when male-dominated medicine and Christianity took over -- were especially into it, too.
But I got the impression that those Samhain celebrations were pretty widespread among just ordinary folk. Like, if Beaver Cleaver's family had lived back then, they would have had a big bonfire and carved a gourd and other Samhain things, the way today they might carve a jack-o-lantern and go trick-or-treating.
