I don't think putting honey in your eyes would b a good thing for getting natural color. Natural color of eyes cannot be changed with temporary help. I prefer rather go for colored contact lenses because they are safe and also comes with different colors which suits the day or occasion for you. :)
Honey is used all over Europe & Latin America to treat wounds and cuts, because it PREVENTS infections due to it being naturally antibacterial & antiviral. It is poured into open bed sores to help regenerate tissue, so putting honey in your eyes will not hurt them, but will help moisturize and brighten the eyes. Just make sure you use 100% unpasteurized/non-heated honey. The REAL honey..not the fake high fructose corn syrup stuff.
There is a lot of anecdotal evidence that over time honey can lighten the iris. However, from what I have read this can take years, and there is no research that has been done on this because quite frankly most people could care less about lightening their iris or simply have closed minds and don't believe it is possible.
If you try this yourself, just remember it may take a year or more to see any results.