Providing there was nothing abnormal with your machine I would change companies just because it took 3 weeks (unless you were told prior)!
That seems expensive for an exhaust, but for all I know that could be the going rate at the mo. As for damaging your machine, unfortunately these things do happen but it's never a good thing. Unfortunately quality of service varies widely from company to company. I once put our machines to an organisation who started working on it the second the skids touched the ground, and it would be returned in spanking condition following a full clean and fresh bill of health.