I didn't think of the game as implying anything about what you should do if you see an actual bird in this situation. It's art, and art doesn't have to be literal. Personally, I saw the bird as embodying vulnerability -- the player's or someone else's -- and the choices we make when we encounter that vulnerability.
I didn't kill the bird. I covered it in flowers and closed the game. I just didn't have the heart to! The animation and art are so good and deeply affecting, so it's hard to see it as just a choice in a game, even when it's the choice you want to make.
I really loved this. It's a short experience but hit harder than anything I've played recently. Great job!