They don't destroy SCPs unless they don't have a choice. For reasoning why, see the Chair Cloud of Doom. To wit, if they tried to shred this deer, it might regrow from the splinters, or remain animate as a cloud of ash, which would be infinitely harder to contain.
And it's known as Safe because it's very easy to contain and they mostly understand it. It's an animate deer made out of contageous wood. Keep it locked up and healthy and it's fine. That's Safe.