There are actually several chemicals in the onion that make your eyes water, but they all belong to the enzyme family known as amino acid sulfoxides. When they mix with air, they form sulfenic acids, which are what make your eyes water.

You can destroy the enzymes not only by freezing the onion, but also by cooking it. Enzymes are very sensitive to temperature. Thus, too low or too high a temperature will destroy the onions. Of course, onions are harder to slice after they are cooked!