Under WTO rules the EU can implement the measures if they are supported by appropriate scientific evidence. The aim of the WTO is to try and ensure that measures such as these or other technical or sanitary requirements are not introduced solely to distort trade and protect domestic industries. It is for this reason that the WTO has become involved in adjudicating scientific evidence. Here there seem to be two issues. Firstly, that increasing volumes of trade worsen the environment and second that the WTO is constraining the use of appropriate environment measures.
Economic theory is clear on the first point.
As a matter of principle, trade cannot be held responsible for increasing environmental degradation. Excessive pollution, deforestation and so on, arise from some form of market failure and the relevant policy is that which is most directly targeted at the distortion. Since the market failure which gives rise to the environmental problem does not arise in the process of international trade, the use of trade policies is not optimal. When appropriate environmental policies, which directly target the source of the problem, are in place then free trade is the policy that maximises world welfare. For instance, take the case of an unregulated industry that generates air pollution.