I had the same issue. Alfred is not in my Login Items. It is in my launch agents:
✗ ls ~/Library/LaunchAgents|grep lfred
com.alfredapp.1password.plist
I've unchecked 'Launch Alfred at login' and then tapped the Quit Alfred button. It will quit but about 10 minutes later (i'm guessing) it restarts. This has happened several times in a row.
UPDATE: But then I removed the `com.alfredapp.1password.plist` file and restarted, and Alfred doesn't seem to keep restarting, yay!