How do I change the current Windows theme programmatically?

You can set it using the following command:

rundll32.exe %SystemRoot%\system32\shell32.dll,Control_RunDLL %SystemRoot%\system32\desk.cpl desk,@Themes /Action:OpenTheme /file:"C:\Windows\Resources\Themes\aero.theme"

Caveat is that this will show the theme selector dialog. You could kill that dialog straight after.