There is no protection for unattended devices lol. That's a huge cat and mouse game. It's why I used to use little embedded boxes like ARTIGO's which were easy to stash along with tamper-evidence tricks. If there was tampering, can't be trusted any more. The few times turned out to be a roommate bumbling around for some ridiculous reason.
There are many physical transports to use. My original hack was IDE in a non-DMA mode to get past serial's speed limits. Then I/O offloading onto dedicated, cheap computers to pre-process the data and force it into correct spot. Next step was synthesis of the same onto cheap, I/O-focused FPGA's or microcontrollers before I had to put a pause on those developments.
The guard [1] is the strongest part. It used simple hardware(s), a security-focused microkernel, carefully written drivers, optional middleware for internal flow control, and separate partitions for each logical function. Anything incoming is fully scrutinized before moving on. Certain protections, such as encryption, might be applied automatically. The modular, layered, often FSM-using implementation of each thing allows the highest amounts of analysis and verification w/ many errors provably absent. You can also gradually add advanced security technology as it comes online such as SecureCore, Cambrige's CHERI processor, DIFT, Softbound + CETS, etc.
So, the concept is physical separation into different domains. The computers use what they need to use. The Internet-facing ones typically did use LiveCD's and BIOS's I could protect to a degree (eg oldest boxes had jumpers). If it wasn't LiveCD, it was regularly restored from clean backups. Virtualization, hardening, and mandatory controls used as appropriate but I assume it will be toast. Simpler formats like text, HTML 3.2, BMP, and so on for easy analysis by guard. If complex stuff is allowed, it goes over a data diode so any malware isn't leaking things back.
For a similar approach at network/host level, see Boeing's OASIS Architecture [3] that builds on their high-assurance Embedded Firewall (PCI card), SNS Server (highest rating/field-use ever), and a bunch of custom components/strategies. Post-police-state, I'm basically just swapping out Linux distro's as I can't afford to build my old setups any more. My current R&D is on tools such as crash-safe.org, CHERI (w/ CHERIBSD), and the cryptographic methods that all protect system confidentiality and integrity from hardware up. Been working on verified ASIC development flow to implement them with that being done up to RTL level. Current explorations are High-level Synthesis, Analog Synthesis, and my medium-high-assurance RAD methods for software. Post most of my results on Schneier.com, etc instead of my own blog for impact with some companies copying it without credit that we've seen. I can email you those if I haven't.
[1] https://en.wikipedia.org/wiki/Guard_%28information_security%...
[2] https://en.wikipedia.org/wiki/Unidirectional_network
[3] http://www.dtic.mil/get-tr-doc/pdf?AD=ADA425566