Of course there is a record of your wife in the immigration for working in Doha but it will not affect her application for a work permit if she wants to work in the future. Beware of these PROs who wants extra money from you. Based on my experience, you do not need them. It is important you take care of family RP for her first. Once she is under your sponsorship, the new company she wants to join in will be the one to process all the formalities and documents for her work permit.