From the documentation:
If a filename is '-', it is also replaced by sys.stdin. To specify an alternative list of filenames, pass it as the first argument to input().
So you can create a list containing '-' as well as the contents of sys.argv[1:] (the default), and pass that to input(). Or alternatively just put - in the list of arguments of your Python program:
cat file.txt|python script.py -u - configuration.txt
or
cat file.txt|python script.py -u configuration.txt -
depending on whether you want data provided on standard input to be processed before or after the contents of configuration.txt.
If you want to do anything more complicated than just processing the contents of standard input as if it were an input file, you probably should not be using the fileinput module.