I also think you probably only need to restrict your dependencies. If you have a dep tree like this:
a
|-b
|-c
Then if crate a decides b isn't trusted, c would inherit the same trust rules. This would allow crates to be refactored, but keep the list of rules needed in big projects to a minimum. You just have to add explicit rules for sub-crates which need more permissions. Thats probably not a big deal in most cases.(You might still, sometimes, want to be able to configure your project to allow privileged operations in c but not b. But thats an edge case. We'd just need to think through & add various options to Cargo.toml.)