From my reading, human faecal matter breaks down very quickly in salt water. Whether this is because e.coli and its mates doesn't like a saline environment or due to bacteriophageous elements in the water - or to both - I'm not sure. But when human faecal matter is mixed with fresh water, as with the usual Western toilet, the bacteria have a field day.
Now obviously, in the enclosed waters of a marina, the harmful bacteria may well be introduced in quantities too great for the natural system to cope with, as happens around fish farms, but I cannot see any harm in discharging faecal matter in a tidal mooring or anchorage, where there aren't many other occupied boats, apart from the aesthetics of it all.
As for urine, surely no-one would think it is other than harmless.
I think that those jurisdictions that control boats' overboard discharges except (and accept for that matter!) a 'bucket and chuck it'. Don't ask me why. In NZ we have a rather more practical approach to the use of a marine toilet - don't empty it within 500 metres of the shoreline or aquaculture. So the environmental aspect of using a marine toilet is muddied, so to speak, with poor biology. On the other hand, I'm perfectly willing to be set right on this one, by someone who knows more about it. But I have heard - and of course it may be apocryphal: maybe QLD Gary could find out more - that a yachtsman in QLD successfully defended himself against a charge of illegal discharge by convincing the judge with the science.
Grey water is, IMHO, even less of an issue. Don't forget we are talking anyway about tiny quantities from most boats, compared with houses. If you use plant-based soaps, I can't see that you are doing any harm at all. In some countries you are actively encouraged to re-cycle your grey water into your garden to grow veg!
The third aspect is the one of plumbing and holes in the hull. Getting rid of both of these makes sense and so some sort of on-board 'sewage system' can only be a good thing. I have to say that for myself, who feels the pollution is over-rated and the attitude towards pollution from yachts verges on the hysterical, the draconian US rules have had the advantage of encouraging a lot of clever people to update the 'bucket and chuck it' to something acceptable to most parties and appropriate to most boats. May their improvements continue and their profits sky-rocket!
These, of course, are my personal prejudices backed up by carefully-edited data and I stand to be corrected.