A major concern would be flushing the cooling system within the engine to make sure that the pieces of the impeller are not blocking any of the passages.
The engine that this pump came from had a blockage that most likely caused a cracked cylinder head. This is the worst water pump I have seen:
The other big concern, as you mentioned, is that the pump can damage the crank case. With a non-metal impeller that is unlikely. As the others have said, post a picture if you can so we can get a better idea of the extent of the problem.
Here's a video I recently made when I was replacing a water pump with a bad bearing. This one had a metal impeller. There may be some useful info for you: