Why do sufi allow building the structure over the graves?
As per this fatwah demolition of the upper structure of the graves is allowed:
I understand It'd be a disrespect when blowing up a grave the bones are shattered and body is displaced. But If these things didn't happen then there's nothing wrong in dismantling the tomb.
The body is buried deep and the structure above it was blown up. I don't know if that actually caused any damage to what was buried deep under the soil. I am not praising their blowing up of the whole thing but just saying levelling them should be allowed and even if they did it in a bad manner. Shouldn't it be?
Instead of blowing them up they could do it by other means but look their main objective was to level the graves and to remove kufr, bidah and shirk done in those places.
They blown the upper construction as it seems, not the underground grave. So it's possible they leveled it not lowered it.