okay I did both the General system preferences disable and my preferences in Safari were already set to open the homepage with a new window. I quit Safari and opened it and it restored everything.
open Safari to your homepage and quit it. then go to ~/Library/Saved Application State/ and lock com.apple.Safari.savedState and then Safari should always open to the state that you just locked
note: to lock a file/folder right click it and choose Get Info (or select it & press command+I) and then click "Locked" in the info window.