Is there a way to persistently disable the menu bar in Konsole on Gnome 3?

There are actually two different settings. The one you described in your question, Ctrl+Shift+M or Settings > Show Menubar is for the current window only.

You can disable the menubar for newly created windows permanently by unchecking Settings > Configure Konsole > General > Show menubar by default or by changing/adding

[KonsoleWindow]
ShowMenuBarByDefault=false

to ~/.config/konsolerc