Prevent attacking when using dugout/rowboat, or nerf weapons range to match aniamals and that problem disappears. Sure there are lots of ways to cheese animals, but boat spear hunting is more of an exploit than cheese, as you just watch animals die doing nothing. Other cheeses actually require some effort from the hunter.
And about animals running away, even without re-agro cheese, it's so easy to track them. I think most people hate animals fleeing because it makes aniamals move from "good hunting spot", meaning a place they're reasily cheesed around.