Bypassing a polarity protection diode with a part of a circuit. Dangerous?
The LM358 will allow this, it will not destroy anything. Look at the datasheet, at Absolute Maximum Ratings (I'm using the TI datahseet):


Input voltage: −0.3 to 32V. So that would be a problem, because with inverted supply, input would be more negative than this.
However: Input Current (VIN &lt; −0.3V): 50mA max. So you're fine unless the resistors are low enough to let 50mA of current through the input. There is even a note expliciting the fact that it is not destructive.


However, I see a potential problem with your design!

The LM358 input common-mode range goes from 0 to Vcc-1.5V. With the additional diode drop, it makes 0 to Vpow-2.2V. In your application and given your inputs, I guess you can easily have a high-level voltage above Vpow-2.2V. In this case, the LM358 may output wrong results. You should use another opamp that has rail-to-rail input range instead. Check in the datasheet (with similar reasoning as above) that it can withstand negative input voltage without being destroyed.