Sure, but if Apple assumes that any non-notarized app is malware, then they're not just preventing malware - they're requiring non-malware to notarize every install. And since this is coupled with a new policy where non-app store installs cost money, this means it will be enforced through the notarization mechanism.

It's not the notarization itself that's an issue, but the fact that it's also the enforcement mechanism for collecting fees per-install. It's basically a mafia protection racket where you need to pay Apple to say you're not malware.