For coding agents you simply drop them into a container or VM and give them a separate worktree. You review and commit from the host. Running agents as your main account or as an IDE plugin is completely bonkers and wholly unreasonable. Only give it the capabilities which you want it to use. Obviously, don't give it the likely enormous stack of capabilities tied to the ambient authority of your personal user ID or ~/.ssh

For use cases where you can't have a boundary around the LLM, you just can't use an LLM and achieve decent safety. At least until someone figures out bit coloring, but given the architecture of LLMs I have very little to no faith that this will happen.