Protecting Microcontroller Input Pins from Soft Power Switch
R1 and R2 will limit the current into pins on your uC and this is usually sufficient to protect your device - you just need to check in the spec what that "limit" current is and choose a resistor value that is appropriate given that the uC supply may be at 0V (un powered). The zeners can be left out on this basis.

Reliability is another issue. Switch bounce may cause your uC to switch on then switch off a few times so write your code to be aware of this. 

I think it may be advisable to have a resistor on enable but probably in the region of +10K and maybe this could be higher possibly 100k.

The voltage on the shutdown pin has to be at least 45% of Vin so this shouldn't be an issue.