What kind of solutions are others out there using to protect GPIO pins during boot? I have a sensor connected that is loop powered so it will be applying voltage at all times to the BBB. My thought is to use some sort of FET bus to protect the board. Ideas or thoughts?
As soon as you did not post anything particular about your concern - not a schematic, nor description, the only advice is: do not use any pins multiplexed with other functions and use opto-isolators for any other. In many many cases direct connection works of course. No need in any FETs.