Is input leakage current a valid way to calculate the input resistance of a digital input on a microcontroller?
You can't really calculate a resistance, but using the current directly is a valid approach. Assume maximum current is flowing in or out of the pin (typically you'd be worried about the current flowing out of the pin when the input is low and into the pin when the input is high) and ensure there is adequate noise margin remaining  under those conditions.
The datasheet you linked shows a maximum current of +/-125nA at 85°C.
Keep in mind that the current will typically increase rapidly if the die temperature is higher than 85°C, so a limit of 125nA at 85°C might be more like 1uA at 125°C.