I agree messing around with the sea-floor will probably mess up the local area, but the area of the Ocean is huge. I am not a micro-biologist but your ideas about the importance and complexity of mitochondria is under estimated.

The primary function of mitochondria is the production of ATP which is then used for energy throughout the rest of the cell. Protein coding by the mitochondria, I would guess, is just a way that this very important part of a cell can have a more powerful feedback loop with the rest of the cell. Unless we can create some kind of nano-bot replacement for the creation of ATP in the cell, with all the right feedback loops, etc., just coding the proteins that the mitochondria codes for in the cell DNA will not work at all.