It looks like you might have accidentally drawn one of your transistors connected to the wrong side of S2, since where it is now it will always be connected to ground and always be off. Even with that fixed though, the new circuit you posted will not be able to tell you if S1 is open or closed when S2 is open.
I see three options. One is pulling the node between the switches high (like you have it now), which means you can't determine the state of S1 when S2 is open. The second is pulling the node between the switches low, which means you can't determine the state of S2 when S1 is open. Lastly, if neither of those two options work for you, you could use an output on the A-Star to allow you to switch between pulling that node high and pulling it low; then you should be able to get all the states.
There are a few other things to consider as well. The ATmega32U4 on the A-Star already has Schmitt triggers built into its I/O pins, so you probably do not need to add external ones. Also, you might need to experiment with the value of your base resistor. The 7.5MΩ resistor seems too large to fully turn on the transistors, but if you use too small a resistor it would create a current path for the motor through the transistors.