I don't think you know what phishing means. By "dropping malware on endpoints" I think you mean having a website serving malware? That's not phishing. For an attack to be "phishing", the website needs to be pretending to be some other website that the user trusts. Passkeys completely prevent the user from logging in to another website than the one they've created an account with.
Your attack only works on people who basically "trust any website" at all. For those, yeah there's no salvation.