As the output of microcontrollers can go very near 0V, you could just attach multiple resistors form the prog pin to IO's. And turning the IO's from an intput (high impedance) to an output set to 0. If you wanted to control the charge current, two in parallel, or three could be used, but ultimately you would just need one IO for charging, or not charging.
Note: those microchip charger chips are great, but do have a limited charge current capability. If you're charging batteries over 1200mAH, it may take a while, as they will limit current based on the temperature of the chip (with sot23-5, that is around 260mA).