The issue is about whether the animal is forced to endure pain, not weather we eat it or not. The same is true for how we keep the animals we eat, and why people are rightfully upset about how some cows and chickens and the like are kept during their short lives before slaughter.

Essentially, having the animal be free before we catch and immediately and hopefully quickly kill it for food is fine. Keeping it in a zoo where it's not suffering is fine.

Keeping it in poor conditions before we kill and eat it is not fine. Keeping it in poor conditions in a zoo is not fine.

This story is interesting in that it gives insight into the mental state of these zoo animals, something that is often hard for the public to see and understand. It should make you pause to consider if we're really keeping these animals in humane conditions, given that apparently even fish have possibly more complex internal mental states than we assume.