Far more complicated than the answer “just reverse the process”, even for inorganic compounds! To reverse a process, the microbes must have the right enzymes and be willing to expend energy to employ those enzymes. Toxic compounds are produced by all forms of life (aerobic and anaerobic) during the process of staying alive. Similarly, all forms of life have the capability of inactivating certain types of toxic chemicals. The chemicals produced  (or activated) and the chemicals which can be inactivated are dependent upon the genes that organism has.

The activation/inactivation of organic chemicals is typically a multi-step process so reconversion from an inactive molecule to an active molecule is not typical.

Nitrogen is a special case. Aerobic microbes convert excess nitrogen in the soil to water soluble nitrate. Anaerobic microbes will convert excess nitrogen to either gaseous nitrogen or nitrous oxide, both of which are released into the atmosphere. Nitrate in the water represents the potential loss of nitrogen and a water pollutant. Nitrous oxide in the atmosphere is bad because it is a potent greenhouse gas, vastly worse than carbon dioxide. Under cap & trade, nitrous oxide will be a major issue

Now to illustrate the complexity of your question, the holy grail of soil scientists is humus. If you slice a humus particle in half and look at the cut surface under a high power microscope, what you see can be thought of as an onion with multiple layers (or bioflims). Organisms growing in the outer layer are aerobic because they pull oxygen from the surrounding soil pore space. As you move towards the center, there is less and less oxygen and more and more carbon dioxide (from aerobic microbial metabolism). So you see layers of facultative microbes (which can live in both an aerobic and an anaerobic environment). At the center, you see anaerobic microbes (even in aerated soils). So even aerobic soils have a significant (and almost totally unstudied) anaerobic component.

Now to answer your question, the toxic chemicals (which are typically only toxic to a particular plant, microbe, etc.) are used for food by other microbes. Carbon recycling!