ADC Measure from source with higher voltage and different ground
If you're that concerned about grounds and accuracy, get an instrumentation amplifier like the AD8221:  https://www.analog.com/en/products/ad8221.html
This would allow you to do truly differential measurements, and, as a benefit, the datasheet shows you how to set up your bypass capacitors to various supplies and grounds.
You can then use the Vref pin to move the instrumentation amp output to the center of your ADC range.
If you don't need hyper accuracy, I'd probably just tie the battery grounds to the microcontroller ground and then run the V+ terminal into the top of a resistive divider like your R1/R2 (10K/10K or 100K/100K depending upon the required ADC input impedance) above and then run the center directly to the ADC input.
The Beaglebone Black, for example, does this on some of its ADC lines because they are referenced to 1.8V instead of 3.3V.
If you really want to be careful you can probably tie the grounds together through a 100Ohm resistor if you really think you might get weird spikes.  A battery probably won't cause any issues like that, though.