Did Pain control the animals from his Summoning jutsu? I'm a fan of Naruto, I wonder if Pain was manipulating his summoned beasts, as I noticed rods in all the animals.
Also, were those animals dead?
Yes!
According to wiki page here 
This is a list Pain can summon :


  The Animal Path (畜生道, Chikushōdō) grants a Rinnegan user the ability of summoning various animals and creatures to aid it in battle. These creatures appear to be immortal, as they were killed and later summoned again
  
  
  Giant Drill-Beaked Bird
  Giant Multi-Headed Dog
  Giant Snake-Tailed Chameleon
  Giant Panda
  Giant Ox
  Giant Rhino
  Giant Crustacean
  Giant Centipede