While you could definitely get away with smaller versions of all the OoT bosses, one thing you'd then have to do is make them less serious and less detailed. Look at 90% of the bosses from the GB games - you'll see bright colors with solid shading and a fairly simple design.
If you're going to stick to that size, you need to a) use brighter purple, like Sprite Collector's, and b) make the eye bigger. It's smaller than Link - players are going to waste a lot of arrows trying to hit that thing.
In my opinion, an edit of Sprite Collector's is the best route - some bosses in GB Zelda are a larger size, and in this case I think you can get away with it.