I had a wood fence installed and when the area was backfilled, soil was in contact with the pickets. The concrete footers for the posts were a few inches below grade leaving soil in direct contact with the posts. I recently did some landscaping along the fence line and I dug the fence out from the ground... I left a 2" buffer between the pickets and ground. I dug around the posts going down to concrete approx. 4" below grade and filled the space with limestone.

I am second guessing myself about digging down to the footers and filling the hole with rock around the posts. Is that OK or will water percolate or collect around the rocks?

 

Unless the water is above the frost level I don't think it will make a difference. If fit reezes, it will have a tendency to push up the post. That is why they try to dig the hole in a reverse dove tail style or wider at the bottom and taper to the top of the soil line.