So my guess is that the main antagonist ...
(who we haven't seen yet but at this point we may have a pretty good idea who it is),
... doesn't really want the Titan-A and it's current crew to be completely destroyed.
It's just going to be stuck in the anomaly, like being in amber.
Imitating how the possible main antagonist was "stuck away" by Picard for many years.
Vadic could have destroyed the ship easily at any point, but was obviously under orders not to.
Perhaps that same entity is also manipulating the rogue changelings?
I wouldn't put it past that entity to do so, since they pretty much did the same with a group of Borg.
I'm also thinking that the old holodeck character may be the one who saves the day.