Measure battery pack cell voltages with analog multiplexer and instrumentational amplifier
The approach is reasonable. Things I'd consider adding: -


Resistors in series with each battery feed to the multiplexer to prevent circuit board track burning when you get it wrong and short the battery out.
Use an InAmp with a small negative rail so that you can avoid having to get rail-to-rail devices (more options are created)
If you implement the series resistors I mentioned then a 10 nF across the InAmp input terminals and 10nF from each input to ground gives you sufficient filtering.
Ensure that the maximum battery voltage does not get close to the peak voltage supply for the CD4052. Max value is 20 volts from the data sheet.
Logic line levels do need to follow the battery supply so use MOSFETs and pull-ups as you mention.
I'd consider using the AD620 as the InAmp but don't forget the small negative rail (circa -3 volts)
For the ADC, the potential divider needs to be calculated correctly and the inherent resistance it provides might be enough of a protection on its own. However, it doesn't hurt to have diodes to both rails in case of over or under voltage.