I certainly hope so. Ocean are polluted enough and although such a ship is just a, well, drop in the ocean, the ideq of accepting to pollute more is unbearable to me, especially for a world class company like SpaceX...
Other than some electronics it's actually pretty clean vehicle - methane will gas off, steel will quickly disintegrate in water, there isn't tons of plastic or paint.
Looking at the composition of the ship, it won't be polluting the ocean much. No people on board to produce trash etc., mostly just plain stainless steel and a bit of ceramics that will make great hiding spot for the abyssal fish for a few years.
