You can run 2 voltage regulators, they prevent this charging phenomenon. I use Jim Oddino's regulator, you can tell him what you are doing and he will match 2 of them so that the 2 batteries draw down evenly, almost perfectly.

Companies like Emcotec make power boxes that take the input from the RX, 2 batteries and route all of the signals for you.

Remember to check both batteries seperately when you power up the plane, or else you could have a latent failure and not know it until you need the backup!