Measuring the cells directly would not be possible as like you said they would all share a common ground through the ADC. You will need to isolate the ADC inputs from each cell using something like an isolated operational amplifier but that would mean that there is a constant current draw on each cell from the op-amps so they would discharge themselves over time.
A bettter option may be to use a dedicated battery monitor which is designed for monitoring and load balancing multi-cell battery packs. Several manufacturers make battery monitor ICs that would work on a lithium battery pack. The BQ76PL455A for example from Texas Instruments can monitor up to 16 cells and communicates over UART so it could be connected to a Raspberry Pi.