I think you may be right that the MCP602 is robust enough to handle over-voltages all by itself given a 1Mohm resistor in front of it. I see the discussion of that now in the datasheet, although my search terms didn't turn it up before.
I wouldn't want to get rid of the op-amp and go passive, though, for a few reasons. First, the sample-and-hold ADC doesn't want an impedance that big in front of it and I'd kind of like to keep it. Second, the ESD protection on the ADC is much less robust than the MCP602's, especially if we are reducing the input impedance. Lastly, using the op-amp gives me an opportunity to filter the signal between the op-amp and the ADC. Also, it is pretty trivial to implement range switching by switching in a different feedback resistor value.
The inverting bit doesn't bother me because you just fix it in firmware.
Even if it's academic, however, is this a protection scheme that is in use?