Because the Champion of Kirkwall passed judgment and for some fucking reason, they're taking that as iron-clad. Even though Meredith was the one to allow that in the first place and she was fucking crazy. And the Grey Wardens do have the legal right to conscript whoever they want for their order, even criminals.

[She sighs heavily, radiating disapproval.]

His repentance means jack shit while he's an abomination; as long as he has that passenger in him, he's a threat to everyone. That's not something we can just ignore.