[parenthephobia]

> this animal is happy and thus does not want to be killed

You're assuming this as a premise, which I think may be the root of the problem. Plenty of people don't believe that livestock is intelligent enough to comprehend the idea of death, or really anticipate the future in general. How then would it have a desire about future events?

> Don't these two sentiments exclude each other?

Wanting something to be happy whilst not respecting its autonomy is common amongst humans, so I'd say no. Additionally, killing an animal humanely doesn't cause it to be unhappy, since dead animals are incapable of experiencing emotional states.