First, taking the city or even just escalating the conflict (either militarily or through underhanded) means is sure to be ruinous for both sides. Last times invasions were attempted, Marienburg defeated the Empire, culminating in the imperial forces surrendering and they had plenty of time to bolster their forces and contingencies since then. As for a covert war, they have the magical know-how and accumulated wealth to hurt the Empire badly (bribing norscans to attack in force, large scale sabotage, etc).
And that's without counting on the fact that desperation could push them toward drastic means should the Empire seem to be winning. It would not be the first time a losing enemy decides they'd rather everybody loses (as evidenced by the current state of the wateland ironicly).
There is no better way to ensure that the End Times happen than strife amongst order faction, but pushing Marienburg to the edge by trying to straight up conquer them (militarily or not) would be one of the worst way to do it.
Marienburg are not villains, on average, their people live better or as well as the Empire's and probably have more freedoms. They were once part of the Empire, but that was generations ago and even thinking that there is a sizable Imperial faction that wants reunification seems overly optimistic (contrarily to the time of the Three Emperors). They fought for their independance.
The currently building canal network will reduce dependance on them anyway. If the Directorate provokes the Empire or Karaz Ankor, let's impresss on them the gravity of their actions, but escalating and gambling on retaking a city that wants nothing of it IS a waste and a great risk.