Flushing Engings

I took my car to my dealership because one of my headlights was not working. While I was there I decided to get a 90K mile check up. It turns out according to the dealer there was carbon deposit build up and the flushed the engine several times without telling me first. Now when I turn on my engine it makes this loud noise and knocks, plus it creaks. They told me this when I went to pick it up and probably there was engine damage and need it to replace the engine.
I took the vehicle to 2 other mechanics and both told me that an engine flush should never be done on a vehicle with 90K or more miles on it, and a car that is not use to frequent oil changes. The car is a 2007 model were they right in what they did?R your question.