EFI guys, any options for theft protection?

First, a short answer to your question. Yes, I'm sure it can be done. Big issue is (apparently) how sensitive the electronics within the system are. They don't like to be meddled with. At least on the ignition side of things. The fuel side is the easier side.

Now when I first started this stuff. If a guy could have made my junk even run well enough for him to steal it. I'd have said good riddance. (OK not really)

But if you could find a way to replicate even a small portion of all the ignition side RF/EMP garbage I dealt with and could eliminate it when you wanted. Then you got something.

I highly doubt that Holleys program is an open source code program so fuddling with it is more than likely out of the question. You could trick it and load a bad program. But what a pain in the ***.