There are a few of ways to work-around this:

1. Manually edit metabase.xml to remove the Web Service Extension
2. Manually edit metabase.xml to change the Web Service Extension to be deletable, then run iisext.vbs to delete it
3. Change iisext.vbs to delete "read-only" Web Service Extensions

Whichever option?you choose depends on what you are comfortable with. I personally prefer #3 because it is the least invasive, and I do not encourage manual editing of metabase.xml. XML is finicky in format so more things can go wrong than right.

Modification of metabase.xml by Removal

1. NET STOP IISADMIN /Y
2. Open %windir%\System32\inetsrv\metabase.xml with an editor like notepad (if on 64bit machine, make sure to do this with a 64bit editor because 32bit editor will be restricted from accessing the System32 directory under which metabase.xml resides)?
3. Search for the word "WebSvcExtRestrictionList" (sans the quotes)
4. Look through the list of items and locate the Web Service Extension you want to delete and remove that entire line. Be careful if it happens to be the first or last item on the list - you must preserve?the leading/trailing quotes of the WebSvcExtRestrictionList attribute
5. NET START W3SVC (and restart any other services that stopped with NET STOP IISADMIN /Y)
   
   Yes, I know there is Edit While Running that simplifies the first and last steps, but I do not like turning on more product features to perform product work-arounds. Remember you are trying to work-around something, so you want less, not more code of that "something" (in this case IIS) running. You can make your own judgement.

Modification of metabase.xml by Changing

1. NET STOP IISADMIN /Y
2. Open %windir%\System32\inetsrv\metabase.xml with an editor like notepad (if on 64bit machine, make sure to do this with a 64bit editor because 32bit editor will be restricted from accessing the System32 directory under which metabase.xml resides)
3. Search for the word "WebSvcExtRestrictionList" (sans the quotes)
4. Look through the list of items and locate the Web Service Extension you want to delete and change its "0" to a "1". For example, suppose I want to change ASP to be deletable. I would change the following:

   1,C:\WINDOWS\System32\inetsrv\asp.dll,0,ASP,Active Server Pages

   to:

   1,C:\WINDOWS\System32\inetsrv\asp.dll,1,ASP,Active Server Pages

5. NET START W3SVC (and restart any other services that stopped with NET STOP IISADMIN /Y)
   
   Yes, I know there is Edit While Running that simplifies the first and last steps, but I do not like turning on more product features to perform product work-arounds. Remember you are trying to work-around something, so you want less, not more code of that "something" (in this case IIS) running. You can make your own judgement.
6. Now run your iisext.vbs /RmFile command and it should succeed.

Modification of iisext.vbs

1. You should search for the following block of code in %windir%\System32\iisext.vbs:

   For i=0 to UBOUND(restrictions)
       If UCASE(restrictions(i).FilePath) = UCASE(strAppName) Then
           If restrictions(i).Deletable = 1 Then
               WebSvcObj.DeleteExtensionFileRecord strAppName
               bDel = True
           End If
       End If
   Next

2. And change it to this (note the single-quote added at the beginning of those two lines):

   For i=0 to UBOUND(restrictions)
       If UCASE(restrictions(i).FilePath) = UCASE(strAppName) Then
           'If restrictions(i).Deletable = 1 Then
               WebSvcObj.DeleteExtensionFileRecord strAppName
               bDel = True
           'End If
       End If
   Next

3. All you did is change the script to delete the Web Service Extension regardless if it is "read only" or not. This should allow you to subsequently run your iisext.vbs /RmFile command to do what you wanted.