When you state "not replacing Bruma" - is this to be in the same location as Bruma, so that the player enters the "other version" through the same city gates? If so, you can duplicate the entire Bruma worldspace and edit the result the way you want - in fact the doors will automatically not be connected to the regular town's interiors, and IIRC the NPC's other than beggars all live in interior cells and will have no AI packages to take them into your cloned space, so much of what you want to do has already happened.
I have done this with an Oblivion world, and you end up with all the content already duplicated, but needing its connections re-established to appropriate copies, e.g. doors not working. There's no easy way to find out what connections are lost, but TES4Edit helps a lot.
Each of the cities already exists as two copies, one in the Tamriel wordspace so you can see it over the walls, and one in a city worldspace. Open Cities copies the detail from the city spaces into the Tamriel one, and adjusts the AI etc. to work with the new locations, so a mod as described above would be incompatible with that, but when OC is in use, the city worldspaces act like the ghost town you describe - no people and the doors don't work, so you may have a compatibility opportunity still!
If it's a Bruma clone in another location, then that will be a LOT harder.