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Wouldn't it be better if the microorganisms on the tongue were completely eradicated?

Certainly not. The bacteria on our tongue and in our month have an important protective role. When they are diminished drastically, say by the chronic use of antibiotics, then the tongue becomes prey to colonization by Candida, a yeast-like organism that causes moneliasis (candidiasis). Candida, which are microorganisms, but not bacteria, are present in small numbers in a lot of our mouths, but are usually kept at bay by the bacteria. Candidal diseases are much more difficult to control than bad breath. So the idea is to keep the number and activity of bacteria on the tongue low, but not get rid of them completely.