Our manuals state that it is permissible to leave passengers on board or to continue boarding if the tire change is being performed by our own company maintenance personnel. If it's done by vendor personnel, we have to go by their procedures, which usually require no pax on board for liability reasons.
For my money, I'd rather deplane the people. A tire change can easily take an hour or more, depending on circumstances, and do I really want people bottled up on the airplane for all that time? I'd much rather they go back in, get a bite, use a real bathroom, and re-board once everything is squared away and signed off. People stuck in a non-moving aluminum tube for extended periods of time have a way of getting progressively more and more pissed off.