How to protect mcu pins from reverse voltage [edited]?
R1 connected in series with the supply is not a good idea. The comparators can draw as much as 2mA (0.8mA typical) and you have zero common mode range to spare. 

R8 also seems pointless- you will get only 2.5V signal from the comparator. 

You can leave R2 in place, increase to 20K and replace D1 with a resistor as Kevin suggests (maybe 2K).