Well the obvious answer to that is to not let the organization crumble. Joss has done it before, just look at Wolfram & Hart on Angel. i realize thez were never the only bad around, but they were always around through all the seasons and Angel never managed to take them out for good. Of course there we have the supernatural element again, them being so powerful BECAUSE there are some very dark forces around, but, in a setting like Dollhouse there could be other reasons for extreme resilience. Like, the clientelle is supposed to be super rich and well connected, right? A possible solution could be total corruption among very high people which prevents anyone (like Echo) to take out the Dollhouse for good.
I see more problems with the ratings. I know I'm not part of the official target population (as I do not live in North America) but if I were, I weren't so sure I would stay in on friday nights alone just to watch a TV show. And I assume many people my age (or older) see it the same way.