Yes, the permanent marker will come off, in fact you could rub it off (or at least smudge it badly) with your finger right now if you tried.

If it were my guitar I'd have another clear coat of lacquer applied to the body & of course over the signature to protect it for life. Probably two or three coats actually. That way if you decide to keep using it you will be able to buff out the inevitable scratches that will come over time, without buffing down to the actual sig.