Take the flight home after stopping work on the last permitted day. A 2 day delay in leaving is not going to be a problem. If you are really concerned, submit an application to extend your visa as a "Visitor" and cover the two "overstay" days with "implied status".
I have a similar situation as the original poster. Only I leave 2 weeks after expiration of my work permit. I attempted to apply for a visitor Visa on the last day of my work permit and there was a technical error online. I submitted an IT ticket to help rectify the issue. I am still waiting for a response from their IT department. If I leave the country before they reply and help me rectify the visitor application, will I have issue re-entering with my new work permit that is currently in progress? (new work permit was started after the other expired).