Yes, you are right, if the question is about the only Win2000 boot loader, the NTLDR. Just delete it if you want to get rid of it.
But just in case somebody wants to get rid of all the traces of previous installation of Win2000, delete also
boot.ini, bootsect.dos, ntdetect.com, ntbootdd.sys, hiberfil.sys (if exist), pagefile.sys, and WINNT directory itself.
In order to delete the files from DOS uncheck or remove Read-only, System, and Hidden attributes.
Also boot from Win9x Startup floppy or DOS floppy (with external FDISK.EXE utility on it) and perform a command