The original reason for disabling AP regen on water, using as an exploit to safely regenerate, is moot, as bodies of water in this breath are too small to hide in (and even if they were larger, a water Elementalist can always track you down and kill you). So there's no reason to keep this mechanic, especially since it only ends up resulting in people getting trapped on water tiles.
If this is asking too much, then at least disable walking onto water at 0 AP to avoid being trapped.