The IRS is right on point. File your own return as married filing separately. However, I think you would be well served to include with your return a letter explaining everything that you stated here on this site. Get the facts in front of the IRS and indicate that you are concerned about following the tax law and therefore you ask for their guidance in this matter. In other words ask them if you handled it properly. It's extremely unlikely that you will get a response from the Service, but you have established a record - make sure that you send the return with your letter by certified mail return receipt requested.
I would also send a courtesy copy of the letter to your ex. ;-)
Send a return claiming Married Filing Separately the old fashioned way. You might not be able to e-file after your SSN has been used. Enclose a short letter explaining that this is your official return and you never agreed to the joint filing made by your husband. Since it just happened, they will know you didn't just change your mind after the passage of time.