Each time you kill WPA_supplicant a new instance is created by your connection manager.
You have to disable it before running the kill command.
To disable the connection manager you need to stop the related service (I.e. network-manager, wicd, etc..) using the command:
service CONNECTION_MANAGER stop
Changing the string CONNECTION_MANAGER with the real service name.
After that you can execute the command you wrote but using an handwritten config file. You can use the command
to find examples or documentation about the configuration file.