Automatic ranging current sensing
There is an inherent problem in getting the uA LTC6102 to short out its own input signal. You should try to use the mA one to do this, and put it closer to the source, rather than the way you have it. 

You will need a comparator that has a common mode range that extends to the negative rail, and you'll need to set up a reference voltage of a few mV for the comparator. You'll likely need some bypass caps to slow things down so the comparator can switch the transistor before your MCU malfunctions from the supply voltage variation.