Your points are interesting though, that the tech did get out (If the NSA knows about it, Alpha is able to set up is own version of it in an old power plant, etc.. then surely it's out somehow), and it went viral somehow. I'd be interested to know how long that took, and what they did in the meantime. There were hints in the Epitaph episodes that it could go either way, being a few years to being somewhat recent, considering the lack of a large number of people at Safe Haven (compared with the number of people that departed the L.A. Dollhouse for Safe Haven), I'd almost hazzard a guess that the mass wiping didn't happen to overly recent. Of course, a lot can happen in a short time, particularly in a situation such as that. I have to wonder if they went 'business as usual' for a while? With the mainframe down, and the recent version of Clyde down, that is the one that knew who did what, the rest of Rossum/the other Dollhouses may not have known who had done it.
I'm thinking this somewhat happened, considering the flashbacks in Epitaph One, which clearly had to be set post destruction of Rossum mainframe (as we knew it) and the fall (Dominic's conversation with Adelle) and slightly onwards.
Of course...those flashbacks were memories, and may not have been to accurate...