I have uninstalled 2000 after installing 2005 as a named instance. It did not kill my machine.
Having said that I always have a roll back plan (a backup and a plan of how to fix it if it brakes)
Is this a production server? IF so you need to be concerned about moving the data and then reconfiguring the apps that use simultaneously (more or less) so that you don't lose data.
David Lundell
Principal Consultant and Trainer
www.mutuallybeneficial.com