You can ask judge's permission to amend your complaint (ask for a leave of court) at any time. If you did not make any amendments yet, it's almost guaranteed that the court will grant you leave. Try it, even though I do not think it is necessary to add DOS as a defendant. If the USCIS requests a visa, DOS should issue it. AGC4Me made great arguments in his MSJ, I did not have anything to add.
Thanks lazycis. I hope that you'll stick around for a long time to come even after your case is closed. Actually at least stick around until my case is closed