My Japanese maple is dying of bacterial wilt and leaf blight and I am certain it will be gone either this fall or next year. Could I plant amelanchier canadensis in it place right away or I need to wait a few years or remove as much soil from the hole before planting? Is there any wilt-resistant small trees that you could recommend?
This year has been a strain on many trees, with drought weakening the xylem feeding route of trees and shrubs. Your description indicates that the Japanese maple you have has suffered greatly. Before considering replacing it however, you may want to determine for yourself if it may be worth saving.
“Growing Wisdom” YouTube June 20, 2016, shows how to prune to save a tree which may be only partly affected.
If you choose to remove it anyway, you will be pleased to know the garden need not be bare in that site. You wisely chose to replace it with a native, the beautiful Serviceberry, Amelanchier canadensis. According to Iowa State university, if the disease is verticillium wilt, there is nothing needed to repair the soil conditions. Verticillium wilt lives in the soil, and attacks fragile or weak specimens. The native tree should be fine as a replacement.
http://www.extension.iastate.edu/verticillium wilt