High Voltage differential Measurement
There are off-the-shelf solutions to this problem, you don't need to mess with transformers and exotic circuits. You can take advantage of the fact that it's much easier to isolate a digital signal than an analog signal and use serial communications between your microcontroller and the battery monitor. You should search for a "multicell battery stack monitor". As an example, the Linear Technology LTC6802 can monitor the voltages on up to 12 Li-ion cells and provide the voltage data via an SPI interface.