1). Get a noc from the travel agency that they have no objection to transfer her to your personal sponsorship.
2) fill in the application form attach passport copy of the maid, the approval number, and original noc from the agency along with your id copy.
3) Go to the immigration department and submit this application and pay a fees of Qrs. 300/-.
You should get your visa in 1 day if all papers are in order. Once you get the visa again visit the imigration with your visa copy and her original passport and they will transfer her visa on the passport again you must pay 500/- for transfer. Thats it after this proceed with medicals and fingerprint.
The agency is probably asking you her original passport as assurity that she wouldnt run away or something like that.