I'm no friend of Best Buy's selling techniques, but I don't think $30 is a completely unreasonable charge. Sure, it only takes a couple of minutes to update an installed and running PS3, but if they do it at Best Buy they're going to need to:
Unbox the PS3
Attach power, video, and internet
wait for the thing to boot
initiate the update process
wait for update to install
wait for system to reboot
run some kind of test to make sure the update "took"
poss. including inserting a game disk or something
rebox PS3
This could easily take somewhere between 20 and 45 minutes