You can force the removal of the DFS root informaiton in a couple of ways. You didn’t mention which OS you are using (windows 2000 or 2003) and the methods can differ. I am assuming that you are having problems using DFS to remove it – so I would suggest DFSUTIL.exe. This tool is in the Support Tools which appear on the Windows 2003 CD. Then can also be downloaded from the Microsoft web site if you do not have the CD handy. Here is an article to use DFSUTIL.exe to remove the root:
Incidentally – unless you have rather intimately rearranged SYSVOL within your Active Directory, DFS is NOT used to replicate SYSVOL. The File Replication Service (FRS) is what performs that function. FRS is also used to replicate data for DFS installations. Turning off the DFSHOst service would be a more appropriate suggestion, although I think you will find DFSUTIL.exe will take care of the issue.