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I think its erroneous to apply some thing so human as morality to something non-human. I think it is correct to infer that animals have some semblance of what we call morality, but it would look black when we see it as white. Animals do not seem to fight with the moral implications of their actions, more that they do what they see needs to be done. For the most part animals are primarily instinctual(from our perspective), but then they also feel emotions, like when they get hurt, or are protecting their young etc... So I would venture to say that yes, they are free thinking, because they are in control of their own lives. If they were robotic, emotionless creatures, then dogs would not protect their owners, lions would not have territorial disputes, and monkeys would not groom each other. But they do these things and so much more. I think animals should be judged by the laws of their own world and not the laws of ours. It'd be like trying to preach the gospel to grass.
I think that decisions like this are different from individual to individual. I think that different aspects of our personality, our upbringing, and a myriad of other factors make up our decisions. Free will ultimately decide the outcome because we always have a choice to go against our nature. But not everyone can overcome their own nature.