I always find that eyewitness testimony, especially in that kind of environment, to be testy and not that reliable.
And you would be amazed at the noise that wild life can make in walls and what they can do inside your house if they are able to get in. I had a large snake in the walls and ceiling of our house and the noises that thing made at night used to scare the crap out of us. We had people come in to see and check and we never knew what it was. One day my ex husband had gone up there and there it was, a large diamond python, curled up in a corner. Then come the possums and sometimes mice from the bushland next door make it into the house itself. Sometimes it literally sounds like footsteps running through the house.
Now put something like that in a high stress environment where the idea of spirits has already been introduced to all who enter said house.. The power of suggestion is very strong.
There are many things that can make things move around in a house.
Don't forget, these people are going there with the full knowledge of paranormal things in that house, so whatever they may see will sometimes automatically end up being something else altogether, after all, their minds will be trying to match with what they know of the house.
As for throwing stones and lighting fires. Possums can do that. My former sister-in-law had a possum family living in her roof, and they used to open her son's bedroom window, hop over her sleeping son and the things they did in her kitchen.. Sometimes an orange would roll down the hall on its own or the limes.. They used to like throwing the limes. Wasn't spirits.
Eliminate all it could be. Look at the house itself, who lived there, their history, their experiences, what could lead people to seeing or experiencing such phenomena? Had anyone involved experienced trauma of some sort when they were younger? Was suggestion involved? Trickery? What were the circumstances surrounding all of it and each individual? What time did these things happen? Did they wait for people to get there to happen (always a tell tale sign of fraud)? And so on and so forth.
People who live in the woods know about animals and the sounds they make. These weren't animals. Here's a replay of part of the OP:
"Strange things continued to happen. Stones, seemingly thrown by phantoms, pelted the farmhouse until every window was shattered. When visitors and family members examined the stones, they found that they were smooth and damp, as though they had been flung from the bed of the river that ran right in front of the house. The roof leaked when it wasn’t raining. Mysterious little fires broke out all over the house. “I saw the house take fire upstairs in ten different places at once,” recalled William Fleury, who lived just up the road from the McDonald family. Once the earth moved the very foundations of the house – and only the McDonald house was shaken by this earthquake. Pots and pans inexplicably crashed from the counters and tables.
“At the time of this trouble,” reported local resident William Stewart, “I lived about three quarters of a mile from the place and was present and saw for myself many of these strange things. Mr. Alex Brown, with the others, took a number of lead balls that came in through the window, marked them, tied them in a bag, and dropped them in to the centre of the Channel Ecarte, in about 36 feet of water, and in a short time the ball came back through the window. I was present when the barn was burned and also when a man by the name of Harmon was preaching there. At this time a large stone came right through the door, breaking out one of the panels, and rolled in front of the minister. The stone apparently had come out of the water. A search was made about the house, but no person could be seen. I also saw a loaf of bread move off the table and dance around the room. The owner of the house, John T. McDonald, I know to be a very respectable man.”
As news of these occurrences spread, hundreds of curiosity seekers from the surrounding areas began to visit the house in hopes of witnessing poltergeist activity first-hand – even the Toronto Globe reported the events as they occurred. The McDonalds took advantage of the situation and profited as a tourist attraction until their safety was really threatened:
“I went with my father to see what was going on at Belledoon for I was very young at that time,” H. Drulard later recalled. “We saw a pot rise from a hearth and chase a dog outside and all around the yard. It could not get away from the pot, for it would hit the dog and he would yell and howl with all his might. I saw an old fashioned butcher knife pass through a crowd of fifty men and strike into the wall the whole length of a ten-inch blade. This happened in 1830.”