Sign the package with hard keys and signature.

That's really the core issue. Developer-signed packages (npm's current attack model is "Eve doing a man-in-the-middle attack between npm and you," which is not exactly the most common threat here) and a transparent key registry should be minimal kit for any package manager, even though all, or at least practically all, the ecosystems are bereft of that. Hardening API surfaces with additional MFA isn't enough; you have to divorce "API authentication" from "cryptographic authentication" so that compromising one doesn't affect the other.