After some fiddling with a script I came to this action. Copy and save it in a .bat file:
FOR /F "usebackq tokens=5" %%i IN (`netstat -aon ^| find "3306"`) DO taskkill /F /PID %%i
Change 'find "3306"' in the port number which needs to be free. Then run the file as administrator. It will kill all the processes running on this port.