Yes, Fort Apogee being hostile to the player is intended.
Currently, the Protectorate forces inside the embassy will be hostile to you the moment you attack SRO. However, they retreat inside and fortify their positions only after you turn in the quest, so when you return you'll see that the Free Drones guarding SRO and that the elevator has now been sealed (making the Junkyard the only entrance to the embassy, as you said).
I like the suggestion about the elevator becoming powered off, more so because it has given me some other ideas which might spice things up a bit more. But I'd rather not reveal or promise anything. I'll just mark this down and wait for the right time.