Another method Ive used is to have two seperate grounds.
Set the amplifier circuit ground to 0V, and set your microcontroller ground to 2.4V.
To do that, you would use a 2.4V regulator for microcontroller ground, and a 5V+2.4V regulator for the positive voltage of your microcontroller.
Then just design your amplifier gain to not go above the 5V+2.4V voltage.
Ok maybe not elegant, but it works really well!