class Parent
  include Mongoid::Document

  accepts_nested_attributes_for :childs, :allow_destroy => true
  embeds_many :childs, :cascade_callbacks => true
end

class Child
  include Mongoid::Document
  include Mongoid::Paranoia

  embedded_in :parent
end

ruby-1.9.2-p290 :046 > p = Parent.create
 => <Parent _id: 4eea357c8035444720000010, _type: nil> 
ruby-1.9.2-p290 :047 > c1 = p.childs.create
 => <Child _id: 4eea357f8035444720000011, _type: nil, deleted_at: nil> 
ruby-1.9.2-p290 :048 > c2 = p.childs.create
 => <Child _id: 4eea35818035444720000012, _type: nil, deleted_at: nil> 
ruby-1.9.2-p290 :049 > p.childs_attributes = {"0" => {"_id" => c1.id}, "1" => {"_id"=>c2.id, "_destroy" => true}}
 => {"0"=>{"_id"=>BSON::ObjectId('4eea357f8035444720000011')}, "1"=>{"_id"=>BSON::ObjectId('4eea35818035444720000012'), "_destroy"=>true}} 
ruby-1.9.2-p290 :050 > p.save  # this shouldn't delete the child, it should just set the deleted_at
 => true 
ruby-1.9.2-p290 :051 > p.childs
 => [<Child _id: 4eea357f8035444720000011, _type: nil, deleted_at: nil, hi: nil>] 
ruby-1.9.2-p290 :055 > p.childs.unscoped.to_a
 => [<Child _id: 4eea357f8035444720000011, _type: nil, deleted_at: nil, hi: nil>]