Hm, that seems kinda cool, but it just doesn't feel right. Most of the Monster's in the Zelda series are, well, Monsters. They can't really tell right from wrong because every time to go near them, they eat you, or pound your green hat covered head. I think the only freindy "Monsters" should be the Deku, I mean, they're already both!
Having friendly enimies in the Mario series worked, because it's Mario. Nothing makes and sense and nothing follows the laws of physics and true factual well-fare.
1.) Traveling through "warp" Pipes? Psh, that is so cliche. Pipes are usually only 1-2 feet in diameter, I seriously doubt the Mario bros are that small.
2.) Mushrooms make you stronger? All they give me is bloating.
MOVING ON.
No, I don't believe "nice" enimies should be implemented in the Zelda series, because there's already too much confusion on what's actually factually true or not. This would just screw up the game(s)
(It might break the time-lines too, which are anoying enough.)