To answer the question posed in the "summary" thread, my first reaction would be that the Embassy is one self-contained building. I may be wrong, but generally I believe that's how most modern-day embassies are built. The reasoning, I would imagine, has to do with the fact that it's easier to "control" and monitor one building than it is to monitor 2, 3, 4+. You have one central access point, and so on.
That being the case, it would undoubtedly include a small medical facility for treating StarFleet personnel, a science lab (not too large), the administrative area for the personnel to work (offices, a "command center" type area where the staff gathers to meet in critical situations, etc.), and a full host of diplomatic meeting areas. (For example, you'd want a room where the staff could hold press conferences, a few conference rooms for meeting with the natives, perhaps an auditorium for larger gatherings, and so on.)
I
don't think that personnel should be housed in the embassy itself. This is not, from what I understand, the usual practice for US Embassies -- especially not in non-hostile locations. And while the plan is for the first embassy to be destroyed by terrorists, I don't think that Duronis II is a war-zone, like, for example, some modern-day African countries where we have embassies. I also think this provides better character development to have the personnel housed outside the embassy.
As for defenses: These would come mostly in the form of personnel. There would be an armory, of course, but there wouldn't be any phasers mounted on the building or anything

StarFleet wouldn't build an embassy in a location where they felt that they'd need to heavily fortify it, so if there is a threat to the embassy (as there will undoubtedly be), it would come in the form of mobs, terrorists, and so on. The embassy would defend itself with handweapons, and the light shuttles discussed elsewhere.