ADC differential filter for DC signals
Your front-end amplifier is a unity gain difference amplifier. You are free to choose the reference potential for differential to single-ended conversion. Tie R3 to your 2.5 Reference not AGND.

Your CMRR will depend on the matching of your 5k resistors. See http://www.analog.com/en/analog-dialogue/articles/deeper-look-into-difference-amplifiers.html