How to prevent applying power to I/O pins before BBB ready?
If the sensor is supplied from the same voltage source as the microcontroller, generally there is no problem. It's not a matter of the board being "ready" so much as never applying voltage to an input that exceeds Vdd of the microcontroller.  The actual specification is: 


  -0.5V to IO supply voltage + 0.3 V


So if the IO supply voltage is 0V the input voltage should not be more than 0.3V or less than -0.5V. 

If such a voltage is applied without limiting the current, it's possible to damage the microcontroller. 

Alternatives include adding some series resistance to limit the current or buffering the input with "something" tolerant of voltage applied when power is off. There are digital buffers that are designed for this purpose (they also translate voltage levels), and for analog circuits you can use an op-amp buffer with some input resistance to protect the op-amp.