There are a few ways to do this. One approach is to use P-channel MOSFETs instead of the PNP on your current schematic. Here’s some additional info on this approach. MOSFETs are great because of their low leakage current – and they’re cheap.

I have attached of a schematic to demonstrate this approach. As, you can see, I have swapped out R4, NPN with an NMOS. Thus, when you enable it (MCU I/O pin output is ~VDD-0.45 Pg 87) the NMOS would turn on; thus, allowing you to measure the battery. I found this NMOS to be suitable, it’s priced around $0.065: http://www.digikey.com/product-detail/en/BSS316N%20H6327/BSS316N%20H6327TR-….

The 100k Resistor is used to bias the “OFF” of Q2 on when Q1 switches on under the control of the enable signal.

The two resistors on the bottom right is used as a voltage divider to measure approximately 3.3V. These resistors come in 0402.

From the original circuit that you have, most of the resistors I presumed were for taking into consideration of current leakage, or some sort of precaution. In the diagram that I drew up, the NMOS I chose has a gate-source threshold of 1.2-2V max for it to turn “ON” and from pg 87 of the datasheet for the MCU the Output Low level of I/O pins at VDD=3V is ~0.7V max. So this should work in theory to keep the NMOS “OFF” when it should be.