In a low-flow dedicated system where drawdown cannot be stabilized due to very low hydraulic conductivity what is the recommended protocol?

If there is no way to get the water level to stabilize during pumping, even at a very low flow rate, you can switch to one of two possibilities. Since you already have a pump installed, you can just purge out one to two volumes of the pump and tubing and then collect the samples. Try to keep the flow rate as low as possible to avoid too much drawdown.  You are not worried about stabilization of the water in this case you just want to get your samples. The other alternative if you have a very short water column, is to switch over to a passive or no-purge method.