This is how I solved it.
Using the script from SMS 2003 Recipes and just add code to import from a csv-file I was able to do the removal. The code for the script can be found below.
Thanks Sherry for the tip about the script in book :-)
' --------------------------------------------------------------------------------------------------
'
' Edit the line with strSMSServer with your SCCM server hostname.
' Create a csv file with all the packageID:s you wants to remove, seperate them with a semicolon.
' Run the Delete_Packages.vbs
'
' Remove the ' from " 'wscript.echo "Deleted " & strPackageID " if you want to display a messagebox
'
' --------------------------------------------------------------------------------------------------
dim fs,objTextFile
set fs=CreateObject("Scripting.FileSystemObject")
dim arrStr
dim x
dim y
x = 0
y = 0
set objTextFile = fs.OpenTextFile("delete_packages.csv")
Do while NOT objTextFile.AtEndOfStream
arrStr = split(objTextFile.ReadLine,";")
Loop
objTextFile.Close
set objTextFile = Nothing
set fs = Nothing
For Each package In arrStr
strSMSServer = "SCCMSERVER"
on error resume next
strPackageID = package
Set objLoc = CreateObject("WbemScripting.SWbemLocator")
Set objSMS= objLoc.ConnectServer(strSMSServer, "root\sms")
Set Results = objSMS.ExecQuery _
("SELECT * From SMS_ProviderLocation WHERE ProviderForLocalSite = true")
For each Loc in Results
If Loc.ProviderForLocalSite = True Then
Set objSMS = objLoc.ConnectServer(Loc.Machine, "root\sms\site_" & _
Loc.SiteCode)
strSMSSiteCode = Loc.Sitecode
end if
Next 'Remove Package
Set objPackage = GetObject( "WinMgmts:\\" & strSMSServer & _
"\root\SMS\site_" & strSMSSiteCode & _
":SMS_Package.PackageID='" & strPackageID & "'")
objPackage.Delete_
'wscript.echo "Deleted " & strPackageID
Next