You need to remember that Halleck blamed the death of his son during TWBTS directly on Bobby Lee. By Halleck's order, the front yard of the Lee home was turned into Arlington National Cemetary. He hated Lee, and Lee loved his home State of Virginia. This is what made Henry Halleck write this ludicrous order. Call it a father's grief, an obsession, or whatever you like, it was not the action of a stable man.