Does no one know how WP3 was developed?
And rather than renaming folders that will get wiped out on upgrades, again - use the new blog defaults plugin listed above. Even if it hasn't been updated yet, it will be soon.
Or, strip out the parts you want from that plugin.
Also, if there are blogs already using a theme in the /default/ folder, swapping that with another one will fail. Because in each blog's db options, there are *two* fields filled out for the theme they have, one of which looks at the stylesheet name (also called default).