Disable the Amplifier during the flashing ESP8266
SD is pulled up to VIN by a 10kΩ resistor. You will need to pull it down to ground with something "stronger" that 10kΩ - a 1kΩ resistor would probably do it.  

Then you can drive the pin HIGH and override that 1kΩ resistance to enable the module.

You could also modify the module to remove the 10kΩ pull-up resistor (the one right by the VIN label which has 1002 printed on it) and use a weaker pull-down resistor (10kΩ would be good).