Go over to the Passport & Immigration office at Gharrafa with a copy of your father's ID and also of your mother's ID. Get a form filled at the typist centers outside the office. Then submit this form at the office. They will charge you QR 20 and cancel your mother's ID on the system immediately. I guess you can then apply for a visa.
Your mother's ID should have been automatically cancelled once father's ID was cancelled but then possibly the system failed to recognize this.