We don't know the full extent of the System's fleet, and given Starworld was destroyed (or otherwise seriously munted) by Orac in Redemption we'll probably never know.
I'd always taken that as read, but after rewatching Redemption I'm not sure it's true.
The surviving Alta is probably fatally injured (or rendered infunctional) when the guards teleported aboard Liberator are then teleported back just in time to throw their grenades at her, but there's no reason to suppose that does any harm to the actual System computer. Aside from anything else, the other DSV is still functioning fine afterwards (if not for long), and Orac only says he's scrambled the other DSV's weapons systems, not anything else.
From what's onscreen, there's no reason to assume that the System and most of its assets didn't survive.