Well, you are talking about taking a devastated region. That's not the only way to do it, but most of what you observe is fairly intentional and is intended to discourage the "loot to rogue and then TO" approach.
Simply put: Don't do that. TO it directly.
There is one part there that is not intentional and one where most players probably haven't figured it out yet.
Not intentional is that all your friendly TO actions have no effect. In the long term, we will transition from the current "control" and "morale" system to fear and sympathy, just like TOs do, which means they will carry over. But we aren't there yet.
Not figured out is provisions. If you think you have a day of grace, you're doing it wrong. With 100% provisions, you should have 5 days before starvation sets in.
