I was thinking that one could just write a loader that goes from SELF->ELF on load. You then pay the cost on startup. Probably not worth it for one-shot programs like ls/cat/etc, but for long running programs and daemons it might be workable.
All of the benefits of SQLite disappear once one diverges from the format in any way. At which point it would be better to ask: "what is the best first-principles implementation of this idea?", instead of "what is the minimal change to SQLite to achieve this specific narrow goal?"