Other than boiling water to make tea and the like, the only case I'm aware of regarding boiling pure water is the Jains boiling water.

However, it's hard to say whether this was "before germ theory," since their religious dogma included the idea that microscopic organisms ("nigoda") lived in water. The reason for boiling water, though was not to avoid illness, but rather to avoid the violence involved in drinking water filled with microbes. (Boiling water and thus killing everything in it is believed to be less violent than drinking water that still has life, for reasons involving a repeated cycle of life and death creating more suffering than a single killing with boiling, although the reasoning isn't entirely clear to this non-Jain. Talk to your local neighborhood Jain theologian for more info.)

There's always room for discussion, but perhaps the section Drinking Water in our FAQ will answer your inqueiry.

Several histories of the transcontinental railroad in the U.S. mention that Chinese workers would boil water for tea, while white workers would drink directly from local water sources, and that water borne illnesses were much more common in the white workers than the Chinese. But I do not recall any mention of it being a deliberate idea of boiling the water to make it safe vs. to make tea. The idea it was the tea that was healthy, not the fact that you boiled the water.

According to Herodotus, Cyrus the Great drank exclusively boiled water from the River Choaspes. He even traveled with it, storing it in silver jars when on military campaigns.