I think if your employer, on his application, has been issued the visa in your name, you still have to go through all the formalities/restrictions as any other employee whose contract was terminated or the employee him/herself resigned regardless the visa was stamped on the passport or not.

Anyway, my suggestion is to act wisely in a tricky situation like this. The best advice could come from someone who is experienced in HR/Admin here in Qatar.

Best of luck!