I would email the accounting manager and cc the GM of the hotel on that email. In the email very concisely explain that you have been double charged for the stay, and tell them the exact amount that needs to be refunded to your credit card. In cases like these I would prefer to do everything in writing- IMHO it is not appropriate that the hotel has placed the burden of contacting the Accounting manager by telephone on the OP- this is the hotel's mistake and they should sort it out.

If the charges are not promptly refunded, then I would dispute this with the CC company. Double charging the OP after check-out without having him/her sign a bill at the property constitutes an unauthorized charge, so this one should be easy to dispute if need be.

Save the original confirmation/receipt for the prepaid reservation, the folio for the stay at the hotel if you still have it, and all written communication with the hotel from this point forward.

edit- I would also send another email directly to the GM to inform him that he has been CC'd on your email to the accounting manager. It might also be a good idea to let the GM know that you were inconvenienced by the strike and did not receive housekeeping during your stay.

I hope that you get some kind of compensation in addition to a full refund of the unauthorized charges.