Why was the Civil Defense Council of Iceland trying to cool the lava from the eruption on Heimaey? In particular what were they trying to protect?

I'm not sure this answers your question, but here are two references to cooling the lava.

1) Thorbjorn saves the harbor by cooling lava in the path of the moving mountain.

2) Cooling lava flows cost one and a half million dollars. It provides thirty million dollars in heating, harbor improvements and paving materials.