The whole point of it replacing great merchant is that the coral port UB has two merchant specialist slots and generates points towards great persons ie the coral ports generates Dhows. I think that this makes the Kilwa civ interesting as it will be a civ that benefits from having many cities along the coast (large empire) but it will also focus at specialists which usually only smaller empires does, it will benefit from Liberty, Patronage, Commerce and Freedom social policy.
A military unit could be interesting though, in that case would the coral port UB have to be changed, and the I am not sure if you could script a military unit to perform trade missions. But if i could be done would it probably be a cheaper, earlier version of the galley, but much weaker and able to conduct trade missions.
The trait: "embarked units can defend themselves, +2 gold per trade route"
Makes the civil unit less vulnerable in the water, so that issue is already solved.
Pouakai: have you tried to start a game with the dhow to see if it works at all?
ShahJahanII: I will post a suggestion for a Marroco/Berber/al-Magrib civ soon your ideas seem intresting. About the kilwa UA/trait, the bonus you propose seems like a good idea but it demands lua scripting, some of it effects is already there indirectly, the coral port (replaces harbour, have three merchant specialists slots and generates two great person points, gives+1 culture for ivory, gold, silver, pearls and spice tiles worked by the city) will be a huge imitative to build your cites along the coast, and the +2 gold per trade route along with the trade route connecting affects of the a harbor in itself gives a huge trade route income because you don't have to pay for road maintenance. And the kind of city states that you are most likely to befreinf is martime beacuse they are always on the coast.
But if you can script other traits in Lua would that be very interesting for this and other civs, please join our 'Terra Novus' group and the 'Zambezi thread', just ask CivOasis who is moderator.