As you have forseen, a multiplier stage cannot be easily deactivated, largely because the control switch has to deal with AC current. Controlling mosfets in the diode positions will not be effective because they only control in one direction.
You already have rectifiers in the circuit. By locating suitable inductors on each phase, before these rectifiers, a single PWM'd boost switch located after the rectifiers can be used to transform the apparent impedance of the battery load. This is easily disabled at higher input voltages, simly by turning the switch off completely.
Examples in this survey by Jang and Jovanovic:
RL