The CreateTextFile method has a third parameter which decides whether file be written unicode or not. You can do like:
var flOutput = fso.CreateTextFile(strFullPath,true, true);
Interestingly, way back I had created this little script to save files in unicode format:
Set FSO=CreateObject("Scripting.FileSystemObject")
Value = InputBox ("Enter the path of the file you want to save in Unicode format.")
If Len(Trim(Value)) > 0 Then
    If FSO.FileExists(Value) Then
        Set iFile = FSO.OpenTextFile (Value)
        Data = iFile.ReadAll
        iFile.Close
        Set oFile = FSO.CreateTextFile (FSO.GetParentFolderName(Value) & "\Unicode" & GetExtention(Value),True,True)
        oFile.Write Data
        oFile.Close
        If FSO.FileExists (FSO.GetParentFolderName(Value) & "\Unicode" & GetExtention(Value)) Then
            MsgBox "File successfully saved to:" & vbCrLf & vbCrLf &  FSO.GetParentFolderName(Value) & "\Unicode" & GetExtention(Value),vbInformation
        Else
            MsgBox "Unknown error was encountered!",vbCritical
        End If
    Else
        MsgBox "Make sure that you have entered the correct file path.",vbExclamation
    End If
End If
Set iFile = Nothing
Set oFile= Nothing
Set FSO= Nothing
Function GetExtention (Path)
    GetExtention = Right(Path,4)
End Function
Note: This is VBScript code, you should save that code in a file like unicode.vbs, and once you double click that file, it will run.