Just thinking out loud here: I wonder if you couldn't just fold the membrane at the keypad, bringing the controller board back to the main part of the keyboard. Then, insert a piece of paper between the layers of the membrane just for the keypad part. Of course, you'd have to get creative with wiring to keep the controller board upright.
I haven't seen a model M membrane. If there is only one connection from the membrane to the controller, you night be able to cut out only the keypad part with no connection, and just fold over the part with the connection, provided the cut-out section has no critical traces running through it.
Of course, none of this has any chance if the connector spans the gap between the keypad and the rest.
Makes me wonder how hard it would be to make a membrane.