Shutdown should safely stop all CPU processes.
Here’s the Linux link for shutdown commands
http://www.computerhope.com/unix/ushutdow.htm
I think two buttons is the only way to do a safe shutdown and completely power off the controller.
I might also put on some external LEDs so I can see the state of the Pi (booting, shutting down, off, on ) because my case covers the on board LEDs. It makes it a bit easier to visual see what’s going on but that requires a little more experimenting and some more components to solder