I understand that chlorine ...

I understand that chlorine is very popular and has been used for donkey's years. There are several drawbacks in treating effluents with chlorine.

Firstly, chlorine is an oxidizing agent but absorbs only 2 electrons. Its residual presence in water is very short. This is because demand for chlorine is high and it is consumed rapidly in water.

Secondly chlorine will react with organics in the wastewater producing chloroform, which is a trihalomethane and carcinogenic in nature.

Even if the contact time is increased it will be ineffective as it is consumed very rapidly in water.

Thirdly, as water biologists we always consider the effectiveness of chlorine in penetrating biofilms. While chlorine might partially treat the e. coli in the water it is unable to do so completely. Then there is the matter of biofilm that is formed in the tank or pond where the effluent is held. 

Chlorine can never penetrate the biofilm and therefore after some time the chlorine gets exhausted, at which time the microorganisms break out from under the biofilm and increase the colony count of e.coli in the water.

Chlorine is just not the right biocide to treat effluents with high microorganism counts. 

While there has been suggestions by others to treat using UV or Ozone both have their limitations. While UV is good for disinfection at POU (Point of Use). This means at the point UV treatment is carried out it must be used either for irrigation or for discharge to the drain. If you store the water the e.coli will grow back as there is no residual presence of the UV in the water.

In case of Ozone it is slightly better. While it has the oxidation capacity of O3 this also is one of its drawbacks. At the point of entry of Ozone in the wastewater you will get very good disinfection but as the gas dissipates its efficacy drops and once there is no more residual left in your wastewater the e.coli will grow back.

Ideally you should be using chlorine dioxide, and chlorine dioxide is not chlorine. Chlorine dioxide is a gas and is more powerful than chlorine. It is able to break the biofilm in the system and completely sanitize the water system, thus not allowing any e.coli to remain. If the cell wall and the nucleus of the e.coli are removed there is no way for the e.coli to grow or mutate. This is what chlorine dioxide does, which neither chlorine, ozone or UV cannot do. Besides this chlorine dioxide will remain as a residual in the water thus if there is any re-contamination of the wastewater it will continue to disinfect.