The Church and the cult of Mullenkamp are clearly in conflict to start with. Most of this information is in the introduction cut-scene. There is apparently a power struggle in the land, and Parliament is too weak to do much.
"All because of this religious freedom! Too much freedom, too many gods! Let those cultist cur-dogs run loose and they will bite you! Gods! While our Parliament cowers -" - VKP Officer
It is not widely known that Mullenkamp and the Duke are in cahouts.
"Our Inquisitors have found that Mullenkamp's coin comes from the captive Duke himself. Indeed, Valendia might still be at war with itself, were it not for the Duke's heroism, yet he wields much of his power from the shadows. Even after his retirement, his grip on Parliament is unrelenting." - voice in VKP meeting
The Duke has control over Parliament (which, in combination with the Church, seem to wield most of the power in the land). The storming of the manor is being used to further the cause of Mullenkamp's cult, by taking hostages and demanding the abdication of the Cardinal.
"The scum make two demands: the release of their imprisoned comrades and the abdication of Cardinal Batista." - VKP Officer.
But why? Why go to all this trouble? Sydney's desire to destroy Lea Monde or relinquish the Dark and free his line from the burden of the Dark is being kept a secret from the rest of the Mullenkamp cult. He needs to convince the cult that there's something the Duke has that will give them the upper hand. But there's more to this.
[Grey Hardin, through Merlose's power] "He sought to seal off our wellspring, after two decades of toil."
[Merlose] "He sought to seal off our wellspring..."
[Hardin] "You..."
[Grey Hardin] "The duke is mortally ill...He fears he will pay for his life's sins in the next. So he seeks to bury this city, as though that would bring absolution."
[Merlose] "And you seek to pluck the city from his dying hands, correct?"
[Merlose (to Hardin)] "Why? Why did you take the manor?"
(Hardin gives her no reply)
[Merlose] "You will answer!"
[Grey Hardin] "To inherit the city, you must have the 'key'. Only the bearer of the key can receive the power of the Gran Grimoire."
[Merlose] "The key?"
[Grey Hardin] "The key-bearer, the Duke, will soon die. If he dies without a successor, all is lost. The Duke thinks he can cut off the cursed Mullenkamp bloodline, but that must not be allowed to happen. We will assume the legacy. Sydney is -"
According to what Hardin knows from Sydney, the only way for Mullenkamp to survive is for the power of the Dark to be transfered. However, Sydney just wants the city destroyed and the curse not to pass to Joshua.
[Hardin] "Only he who holds the Blood-Sin can succeed to the Dark city. The would-be successor must cede his phantom soul if he is to accept his
prize - control of the Dark. These streets already teem with souls. All that is needed is the key. We have no time. The key, show it to me."
Hardin believes that Sydney is trying to gain control of the Dark to help Mullenkamp. Sydney has Hardin fooled. This is futher evidenced by
[Hardin] "Are Riskbreakers all this powerful? Syd: (gets up) I think not. Our Ashley is a vessel, you see. He has merely partaken of the power around him. It is as I have forseen."
[Sydney] "What next? Let him give chase a while."
[Hardin] "This is madness, Sydney!! The Blades will hold this town soon, and we dare not face their undivided forces! We've no time to play cat and mouse!"
[Sydney] "Relax, my good Hardin. Remember, it is all part of my plan."
[Hardin] "Were the Duke's betrayal, the cardinal's meddling...and a Riskbreaker strong as a bloody titan all part of your precious plan, too, Sydney?"
Going back to the beginning, Sydney and the Duke seem to have convinced everyone that there has been a betrayal, and that the principal source of Mullenkamp's power (at least financial). The raid on the manor was because Sydney told his cult that the Duke had the Blood Sin, and they key to the Dark power at the wellspring of Dark that is Lea Monde.
[Rosencrantz] "You're a slow one. Sydney is increasing the flow of Dark energies on purpose."
[Grissom] "Why would he?"
[Rosencrantz] "That is the question..."
[Rosencrantz] "Didn't everyone? The city is the Circle, the "wellspring". And the "book" - the Gran Grimoire - for which you seek...You're standing in it. Leà Monde is the Gran Grimoire!"
Taking this into account with the earthquake 25 years ago, it seems that it wasn't the earthquake that caused the wellspring of souls, but rather the wellspring souls that caused the earthquake at Lea Monde. It makes sense, then, that in order to destroy the city, another wellspring of souls would need to be taken. What better way to attract a large group of people than to start the raid on the manor?
It seems to be a happy accident that Ashley was found to inherit the Dark. That he was a perfect inheritor to the Dark changed Sydney's plans midway so that the Dark would not accidently fall into the wrong hands.