Doc hates this, trying and failing. Even if it's Souls, it's still murder. They die in pain, even as he tries his best to make it as quick as possible.
Because he can't give up. This is their only hope of survival, this little experiment into the Souls and even if it kills both the Soul and their Host they can't stop trying.
They need him to carry on, no matter how much he hates it, no matter how much it goes against what he believes.
He patients are literally dying in his hands and he does it again.
As Einstein said, it is the definition of madness.
And it breaks his heart.