Clean restart from terminal?
Yeah, ok.  I can solve this with Applescript.  Thanks to patrix for getting me to look in the right direction.

tell application "Finder"
    restart
end tell


Saved as restart.scpt, run with osascript restart.scpt. I've tested running it remotely with the screen locked, and it restarted cleanly perfectly. I need to remember that Applescript exists whenever I want to automate Finder interactions..