The OP did the right thing by filing as married. She did not commit a fraud, and the CRA will not see it as a fraud. She is married now, so should indicate that on her income tax return. She does not otherwise have to inform the government, since she is already a PR.
Now, the problem is since she is married, the CRA wants to cross-check her and her husband's return. Since he is not in Canada and did not file a return, such a thing is not possible. That is why CRA sent her the letter. She will have to write them a letter explaining that her husband is living exclusively outside Canada, has never been to Canada, is a citizen of ..., and does not have a SIN. (Supposing all that is correct.)
The likely impact (of filing as single when actually married) is low. There is a slight chance CIC might question why you are listed as single on the Option C when you claim to be married to the applicant - if they notice. However, there is no reason not to just honestly admit you are married on your tax forms, in which case your Option C (which you need when you sponsor) will list you as married.