Windows batch files are a lot more limited which limits options compared to bash's ability to run the application as a job in the background while the script keeps running.
One way it could be done is by running the script again through the 'start' command, with perhaps the path and process ID as parameters along with a parameter to make it run in this background mode, and let that separate part of the script take care of the killing when the .kill file is synced in.
I have yet to find time to implement this, but it'll come sometime soon.