2000 Isuzu Amigo 2000 Amigo engine problems

I have a 2000 Isuzu Amigo with a knocking noise in the engine. It only has 42000 miles on it. It started about a week ago so I checked the oil and it was low so I added oil but over filled it mistake the noise did go away for a day or two but returned so I took it my shop at first they said they could flush the oil system out and see what happens an hour later they are tellin me I need a new engine By the way the check engine light just came on yesterday and the car is still drivable. My question is do you think I can just repair this engine or do I have to get a new one. Thank you for any help you can give me