I wanted to possibly leave these configurable as output pins, but that would potentially leave the microcontroller connected directly to 9 volts if I build it as per the instructions. Might this hurt it?
If you follow the instructions properly no microcontroller pin will see 9V. 9V is too much for the inputs/outputs and you would likely damage the micro. That is the reason for the voltage regulator.
If you configure those pins like the tutorial with power buses and try to change the PortC (sensor) bus above 5V then you will not be able to use any of the pins as analogue inputs with that bus (actually you can, but it is not simple to do). How likely is it that you will build a 'bot that doesn't require analogue inputs? Could you not add extra headers for the unused pins (9:14) for extra IO? After that you could relocate the ISP header and use pins 15:19 also.
How would it affect the sensors to be hooked up to the lower voltage?
It depends entirely on the sensor as to what voltage it requires. From the point of view of the micro a voltage below 5V will not hurt it, but you will not be able to use the full voltage range of the ADC and so will not have the full 10 bit precision available. This is usually not a big issue.
I could hook up a switch so the 9 and 5 volt levels could be toggled between, but unfortunately that would be easy to mess up during usage....
Yes you could, I like to use a jumper to select different bus voltages as it is compact and fits well with the existing headers, but a switch would work fine too.