My understanding and my interpretation of the way it's currently drafted is that the proposed subsection 35(2) that will come into effect with the legislation passing is strictly a clarification of the definition of a harmful alteration, disruption, or destruction of fish habitat. Essentially, they've added a comma to that definition so that it's understood that your disruption of habitat needs to be harmful to fish before an authorization is required.
The second part is the bringing into provision the serious harm aspect of subsection 35(2), which essentially prohibits serious harm to fish, and that is the death of a fish or any permanent alteration or destruction of fish habitat.
Currently, the prohibition is the destruction of fish, so DFO could essentially charge you for destroying a fish that's already dead.