That should not be an issue whatsoever with 2 John Smiths, two should should up and you click on whichever one you want. Most people I know actually deactivate the activity system. When they message the private message by clicking on profile, most communities are not the type everyone knows everyone, its actually the other way around, those types are in minority and buddypress seems to cater to them.
Its actually a very simple solution, implement an option, with username and another one first and last name.
