Ceiling Fan update with Metal Sheathed Cables and Romex
Since you have access to the box from above a ceiling fan box would be a good and easy replacement. 



The wires only look like they have metallic sheathed, they are not.

If you feel strongly about damage to the wire you can always replace it. As long as the insulation on the inner conductors is not damaged the wire should be fine. 

Yes, the two kinds of wires can be used together.