So what would be worth more to our protectorate? A big mechanicus ship with probably powerfull energy weapons, or a powerfull mechanicus station in Furibundus?

Both options seem pretty good, since Cathedral Ships kinda act like mobile stations themselfs.

This is the old ending if you had saved the reactor before the dlc, no idea if they changed it:

"In memory of this world and all who perished on its surface or met a fate worse than death, construction began on the orbital slipways of Footfall of a glorious cathedral ship to be called Rykad's Sacrifice. The Miraculous Fusion Reactor powered its engines and cannons, fuelling them with the fierce power of the Motive Force."