Everyone has different tastes. As a professional designer whose tastes seem to be aligned with those of Apple's design team, I LOVE the look of the black MacBook with the white Apple logo. Just like I LOVE the look of a Gibson Les Paul Custom Black Beauty, or the Parker Fly in all black with it's white logo. To me it represents the perfect balance of great design and branding.
That said, there's a MacFixIt page where they show you how to disassemble your MacBook. Of course it will void the warranty, but if the color of the logo is important to you, then it may be acceptable.
Another thing you could try is using an adhesive-backed colored gel or mylar of some sort, and honing your exacto skills to cut two pieces of precisely trimmed overlay. Then, later if your tastes determine it was not so "garish" after all, you can remove them.
Might be cool to have one color for the Apple, another for the leaf/stem.
Red Apple, Green leaf/stem. Purple or indigo Apple, Yellow leaf/stem.
It would work, I think. I know that there are some clear adhesive films available:
http://www.misterart.com/store/view/001/group_id/656/ULANO-Masking-Films.htm
http://www.misterart.com/store/view/003/group_id/313/GRAFIX-Funky-Film.htm
or if you want to go black, this looks interesting. Some are labeled as "solid" referring to transparency, however, it is most often not the intention of the manufacturer to have them backlit.
http://betterthanpaint.com/store/category.php?CATEGORY=1
Or you might try Rubylith or Amberlith:
http://www.misterart.com/store/view.cfm?group_id=656&store=001
In any case, you may want to try to go this route, detailing what you did, and maybe post images so that others may accomplish it.
An enterprising young person with a good die cutter could actually make a business outta this!
Bob