Why won't a simple controller re-assignment work? From the sounds of it, the PS3 picks up the USB receiver and assigns it controller port 1 (the only port some games will recognize for input). USB devices get priority with controller assignments on the PS3 at boot up for some reason (faster recognition, maybe). However, the PS button should still work on any BT controller (which will get assigned to controller 2). Pressing the PS Button on the BT controller should bring up the XMB. From which you can go to Settings and then change the controler number to 1. Conversly, holding the PS button on the BT controller will bring up the original in-game menu, which makes controller re-assignment even faster. All without exiting the game or restarting the PS3.
Your method sounds like what I have to do on the 360 to change controler assignments when I have a USB controller connected.
I would have thought so too - but when doing this my controller seems to be picked up as controller one as is, but it doesn't do anything once some games are launched while the USB receiver is in. It's not all games (NG Sigma is one, for example, plus some PSN games of what I've tried) but it's annoying enough to make me leave the USB key out of the PS3 unless I specifically intend to watch a movie.