Ships wouldn't need a long submerged pipe. It'd just need a small hole like a bilge drain or maybe a live well on a fishing boat. Just let the boat cruise around slowly draining back into the ocean.

As for surface life, I'm no oceanographer, but is that really the most vulnerable place? The surface is where fresh water rain meets the ocean, so that would dilute the salinity during storms. However, there's nothing to say that another pump couldn't be pulling from the ocean and mixing the brine into that so it's diluted before and not just pouring brine straight into the ocean