I really don't see why it's not possible to just use basically a "highlighter" token which is added to all the authoritative instructions and not to data. Should be very fast for the model to learn it during rlhf or similar.
I have a theory that a lot of prompt injection is due to a lack of hierarchical structure in the input. You can tell that when I write [reply] in the middle of my comment it's part of the comment body and not the actual end of it. If you view the entire world through the lense of a flat linear text stream though it gets harder. You can add xml style <external></external> tags wrapping stuff, but that requires remembering where you are for an unbounded length of time, easier to forget than direct tagging of data.
All of this is probability though, no guarantees with this kind of approach.