I've solved this problem for myself, and I suspect that many other people have it, but nobody has shown any interest in my solution so far:

https://github.com/skorokithakis/gweet

It's a command queue that allows your Raspi/Arduino to listen to commands and your control apps to issue them. I use secret keys for the commands, but you can also use crypto to sign the requests. It's been working very well for me, and with very low latency (the DNS query and TLS setup are the slowest parts, it seems).