Digital Input Clamp Circuit Protection
General guidelines being given are generally OK

BUT

You MUST NOT exceed Vdd with any sort of drive capability.
The 3V9 you quote is an ABSOLUTE MAXIMUM value and your controller may well go gaga if you apply that during operation. Look at data sheet in 'typical operating conditions' section and see what limits there are. In a very few datasheets, probably written by marketing men or the office cleaner, they may say 0.2V or 0.3V outside rails is OK BUT more than 0.small is dangerous. Real designers [tm] say 0.0V outside rails in their data sheets.
Experience suggests that the 1M you showed for R1001 is a good idea if you MUST have Vin > Vdd. Still not marvellous but will more often be more liable to be reliable. 

Some people argue long and hard that body diode conduction at small currents during operation is OK. Listen to them if you don't care about commercial levels of reliability.

Current in body diodes usually flows into IC substrate and may end up in nodes not usually powered an can trigger spurious FET action where no FET usually exists and can noise up ADCS. These effects are insidious and unpredictable and may be fatal to design reliability. Many "RAD hard" parts (you pay for them in gold) and some others may be designed to specifically target these issues but the large majority  are not. 

IF your diode clamps allow input voltage to always be
>= Vin_high_min and
&lt;= Vdd_min_actual
(and equivalent for Vin low) for all legal and likely Vin high (and low)  during operation then you will be better off than dicing with Murphy.