As much as we joke about our armed forces, they are professionals who do their jobs to the best of the abilities...
The problem with trying to assert sovereignty over the cod fishery was a lot of it happened in international waters, and the problem there is... they're international waters. Not even the US Navy asserts domain over half the Atlantic for its own fishermen. Again, we could argue the government should have done
something sooner, but I don't think we can blame the DFO under Mulroney's government for using the most extreme measure available to it to prevent the entire species from dying out in a blink.