On one hand violation of the environmental laws by the company should be punished and this is within the enforcement powers of the agency. The EPA should follow required procedures and cannot go beyond the authority granted by Congress. Provided the estimated risk concerning the health, safety or environmental protection is greater than the economic impact from the plant closure, then the agency should enforce its decision.
On the other hand, shutting down the plant will cause significant social damage, as the plant is the major source of employment for the town. If breach of environmental laws does not represent a major threat to the health and safety of people and has not significantly impaired local environment, then the agency can take restrictive action other than closing the plant, probably by imposing penalties or fines and undertaking future stricter control over the company's operations.
The Environmental Protection Agency requires your company to self-report pollution discharges daily. It is your job to make those reports. The reports could be easily fudged if the company exceeded its designated limits. Excessive discharges would cost the company $25,000 for each day its limit is exceeded.