Yes. The first standard for securing computer systems mandated some protections against this. They were partly made by Paul Karger who invented the compiler subversion Thompson wrote about a decade later. Most just focused on that one thing where Karger et al went on to build systems that were secure from ground up with some surviving NSA pentesting and analysis for 2-5 years. Independently, people started building verified compilers and whole stacks w/ CPU's. They were initially simple with a lot to trust but got better over time. Recently, the two schools have been merging more. Mainstream INFOSEC and IT just ignores it all slowly reinventing it piece by piece with knock offs. It's hard, has performance hit, or is built in something other than C language so don't do it. (shrugs)
Here's several examples:
VLISP for Scheme48 whose papers are here: https://en.wikipedia.org/wiki/PreScheme
C0 compiler + whole stack correctness in Verisoft http://www.verisoft.de/VerisoftRepository.html
CompCert Compiler for C http://compcert.inria.fr/
CakeML Subset of Standard ML https://cakeml.org/
Rockwell-Collins doing crypto DSL compiled to verified CPU http://www.ccs.neu.edu/home/pete/acl206/slides/hardin.pdf
Karger's original paper with the attack from 1970's: https://www.acsac.org/2002/papers/classic-multics.pdf
Myer's landmark work on subversion in high-assurance security from 1980: http://csrc.nist.gov/publications/history/myer80.pdf
My framework I developed studying Karger back when I was building secure things: