It was in no way critical that we get Thorek's aid for the Project, we just figured it would be useful and threw the Middleheim dwarfs under the runic bus. It was also no critical that we gave Boris his smoking gun against the boyars from Praag, we just wanted him to like us more.
Middleheim dwarfs aren't some innocent victims of two power hungry villains.
I'm sorry, but with all our and Thorek's influence we still couldn't "threw the Middleheim dwarfs under the bus" only because we wanted so.
Many dwarfs oppose them because they think that it's right. You heard Thorek's reasons. He do it because it's right for his culture and morale. And we don't have many reasons to think that he is wrong.
We didn't made a final decision, we give Thorak ammo for his case.
And boyars in Praag needed to be investigated. Mathilde themselves thought so. Strong links to vampire, some shady deal that draw attention of evil forces.
Like Abel said, we deal death to the corrupt to prevent the suffering of the innocent.