Yes, I think it is possible to reduce this overcurrent. This is most likely caused by the abrupt change in potential when the cyclic voltammetry test is run with the 'shift' parameter (dimensionless phase shift) set to zero. The cyclic voltammetry test outputs a triangle waveform for the potential and when the 'shift' parameter is set to zero this waveform will start at the minimum voltage as shown in the figure below
This figure shows two cycles of the potential output for the cyclic voltammetry test when shift = 0. At the start of the test the potential abruptly changes from 0V to the minimum value (in this case -0.4V) at the start of the test. This abrupt change in potential can cause a large current.
In order to minimize this current it is possible to adjust the shift parameter so that the waveform starts at 0V and then linearly progresses to the minimum value. An example is shown in the figure below
In this case the shift was adjusted so that the waveform initial goes from 0V to the minimum voltage (-0.4V). The exact value of the shift parameter required to achieve this depends on your minimum and maximum voltages and can be calculated as follows
shift = 0.5*(volt_max/(volt_max-volt_min)) + 0.5
Regarding your second question. There is currently no way to disconnect the counter electrode via the firmware e.g., via some sort of digital switch. However, this is something I would like to add to a future revision of the hardware design. At the moment your best option might be to physically disconnect the counter electrode whenever you remove the reference electrode.