I know of no way to keep minimized windows from being restored when executing a
killall Dock command, by any method.
The long workaround is to enumerate all application processes with visible windows and make a list of all minimized windows before executing
killall Dock and then use the list to re-minimize afterwards. I seriously don't recommend doing that, but it's doable if you want to spend the time coding it.
That said, why not just use a method that doesn't require using
killall Dock and immediately changes the wallpaper?
Here are two examples using AppleScript:
tell application "Finder" to set desktop picture to POSIX file "/Library/Desktop Pictures/Milky Way.jpg"
tell application "Finder" to set desktop picture to alias "Macintosh HD:Library:Desktop Pictures:Sierra.jpg"
From the command line, e.g. in Terminal or shell based script:
osascript -e 'tell application "Finder" to set desktop picture to POSIX file "/Library/Desktop Pictures/Milky Way.jpg"'
Any of these immediately changes the wallpaper without further need to do anything.