I read the published paper in the journal and I think a lot of the criticism about it is unjustified and exaggerated. It's a simple little study (single sample), a "short communication", that simply identifies living sea lice (eggs and nauplii) being discharged at depth in the ocean from the fish processing plant as a potential issue. They know it was during a period of farmed Atlantic salmon processing because the DFO Scale Lab identified scales collected in the sample. Unlike meat processing plants that are required to discharge their effluent into the sewage system, fish processors can discharge directly to the ocean, and always have. I think they raise a valid concern that direct discharge, without effluent or sewage treatment, could be a vector for introducing infection agents back to the ecosystem and they should do further research and look at treating the effluent. Nothing earth shaking here....the only unexpected part of the results is that the filter screens that should remove lice components from the effluent seem to have failed (or aren't in place).
I think it highlights this ancient mindset that the ocean is our dumping ground and it doesn't matter what we discharge to it (human sewage, processing plant waste, agricultural runoff), it will be "consumed" by the ocean.