I remember seeing something like this in photographs of Andy Summers' Gibson ES-335. At some point, the guitar had been converted to left-handed. Later, it was converted back to right handed. Four round marks are clearly disernable around the upper F hole in the front of the guitar.
The hardware store should have something that will fill the hole and look decent - I'm thinking of a metal button that looks like a snap on the outside. My Marshall has a couple where a loop was removed.
I use Durhams water putty. Put painters tape on the finish side, plug cavity with mixed Durhams, let dry. Remove tape and buff, paint, what have you. Stuff finishes like cement and its cheap.
Just unhook whatever you had in there from the circuit; don't bother physically removing it from the guitar. It's the easiest way, the cheapest way, and the best looking way.