Unfortunately in real-life on our planet (Earth) deep sea mining for rare earth minerals is devastating to biological ecosystems and has very little motivations beyond the capitalistic/industrial ones, so I want to find fictional but somewhat plausible humanitarian motives for the organization my protagonist works for to be engaged in this. It could be an alien planet but it has to relate to sea rather than land. It doesn't need to be near the present time, but preferably.
It's not more ethical. It's just as bad, but the mining company decided a long time ago to smooth things out using the good old "public relations strategy". They tried to come up with something, anything, that can be seen as ethical back-up support for their operations. They tried to appeal to some vague ethics and morality, "for the people", "hear the poor", blah, blah.
Excerpts from their propaganda include (but are not limited to):
Mining on the sea will not displace people. The mainland is already full of people. It's better for us the mining company to mine stuffs under the sea rather than forcibly relocating hundreds if not thousands of people in the long run, as an indirect consequence.
Mining on the sea will not disturb environment near humans. There will be no more forests being burnt and cleared for mining ops, just to be abandoned when everything is done and the ores are sucked dry. The immediate effect of mining to human surroundings are unpleasant. Doing it on the sea makes people not aware of it every day of their lives. People likes it better when there are no mining stations situated near them.
Our mining operations are more friendly to fish and marine ecosystem in general compared to it's effects to human day-to-day lives.
There will be no more people protesting because a mining company operating in their backyard gives them benefits that are not adequate nor proportional. Deep sea mining is in international waters, and at most it's still no one's backyard. There are no moral ambiguity as to how our profits have to be spent. Our profits can be more freely distributed and allocated for better pursuit of mankind's happiness.
Oh, and just in case, we'll highlight the fact that our competitors --- who solely operate on land --- do all the negatives we mentioned above. And we'll be sure to exaggerate, just in case our point isn't clear yet.
 Put scientific citations here. The company publishes some sort of "study" whose conclusion agrees with the company's bottom line.
 Another scientific citations but from different names as to look more legit. Claim whatever you want, slightly differently phrased.
 Some other publications that twist the data and statistics in favor of your goals. Pepper some misleading numbers and out-of-context quotes. Slightly pop-science themed to appeal to larger general audience.
Long Term thinking. Like really long term.
As in David Brin's Uplift series your culture has started thinking on the order of millennia instead of days. Recycling via geological undersea subduction is now taken for granted, so undersea mining is permitted in "close" proximity to tectonic plate edges.
It is a part of the Bio-Diversity/reef restoration project. Your planet is in the not too distant future, where due to the climate change, the temperature and other properties (salinity, acidity) of the oceans changed to such a point, that most of the aquatic life as well as corals and other marine biology is on the verge of extinction.
Only way "that is currently viable" is a construction of aquaforming preserves at various places along the bottom of the oceans, which use geothermal as well as tidal energy to restore the ocean conditions (salinity, temperature, acidity) to the proper conditions, for the life to continue as is. These oasis obviously cannot change the properties of the whole ocean, but modify large surrounding areas of ocean sufficiently, for the life to continue there as is, and even spread from it, as the mature populations can handle the non ideal ocean condition.
Originally the preserves were funded by worlds' governments and did not generate any profit, however, despite the objective measurable improvements, it cost such a significant amount of the world economy, it was in danger of being stopped. It has been therefore decided, that during the drilling of (massive) shafts for geothermal heat-pumps rare minerals are extracted for profit to cover (lover) the costs of this endeavor.