I'm not an expert. From what I've read, it is better to hibernate temperate turtles. Then, they live longer and are more apt to reproduce. The thing is that with indoor hibernation in refrigerators, it seems that things can go wrong so it's a risk. Natural hibernation can be risky too. For example, if a turtle picks a pond that freezes solid, it dies. I've never built a turtle fence around my ponds. I've seen a number of designs. Some turtles can climb but most can't so a fence of about two feet high should be enough to keep them in (but won't keep out most predators). Chicken wire rusts within a year so it's not a good choice. Regular fencing (what I call dog fence) has holes that are too big. I suggest hardware cloth (what I call rabbit wire). If you can get the green vinyl coated hardware cloth, that is strong and very long lasting. You would attach that to wooden stakes every maybe 1.5 feet. Be sure that the fence goes into the ground a few inches as turtles can dig.
Hibernating turtles indoors is usually done with a dedicated refrigerator set to the correct temperature for the species (normally in the mid 40's degrees F). The turtle can be put into a plastic shoe box in an inch of water with holes in the lid for oxygen. Check on him every week and change the water as needed. I've not done this myself so please refer to those that have.
You can try your method which may work better as it's more natural. I wouldn't put many if any leaves or dirt in the container as that just makes it dirty. The water quality would be worse. Turtles don't need those things. They just need a place to hide. You can make shelters out of varous plastic pots, tunnels, PVC pipe, etc. Be sure the size turtle can't get stuck in what's in there. I wonder if they make something that's sort of like fake leaves that turtles could use like a blanket for winter? Of course, knowing turtles, they'd eat them!
My page on turtle ponds is at
http://www.fishpondinfo.com/turtles/turpond.htm