Nope can't play them from the SD card. I know it's stupid hopefully Nintendo will release a update or something.
Now there is a reason for it though. Think about having like 50 VC games on your Wii. I doubt you'll be playing them all at the same time, plus I don't think they would all fit so you copy some of the ones that you've beaten or whatever to an SD card. They'll be safe and if you ever feel like playing them again you just copy them back over. Still a hassle but for now it's not that big of deal because there aren't that many games on the VC.