Actually, an interesting way to look at it (and possibly disturbing) is that if said aliens are on another tier of intelligence beyond humanity, then the humans in question might not ever realize they were "pets".
"free will" or not, your dog doesn't know he's a pet. He's doing his dog thing and what he thinks he's supposed to be doing. The context of the human world he finds himself in, is beyond his capability to comprehend.
Likewise, a human placed in an alien context that is literally beyond human intellectual capability, might never realize the true reasons why the aliens interact with him. Or realize his own behavior - which he sees as entirely free - goes right along with what the greater intelligence desires.
In short, you can't rebel if nothing being done to you, or with you, is comprehensible as oppression.
At most, the human might sometimes "dig a hole under the fence" in frustration at some mysterious obstacle that is in his way, never understanding it was put there by his 'master' to control his behavior. And when he was put back inside the fence, he would not entirely understand what was happening.
