I just flipped through section 3 of the manual and couldn't find anything prohibiting the wearing of shorts at the event or in the pits. I know teams have done a similar look to the one you're planning and I don't think they've been hassled about it.
IMO, if you're still worried about it, you can have your actual pit crew wear pants and then have the remainder of the team members that aren't in the pits wear shorts.
Here's a link to section 3 if you want to read into the pit rules some more:
http://www.usfirst.org/uploadedFiles...e%20Events.pdf