Did you use any chemicals like "bee go" to help you remove the bees from your frames while taking off the honey? They tend to leave a terrible smell in the honey (to me it smells like vomit)for a while. But the smell dissipates after a few days and leaves the honey totally unharmed. Even the natural floral fragrance of the honey returns after the chemical smell goes away.
Like all the others have said one way or another, a little patience will go along way.
MOST CERTAINLY, DON'T THROW OUT THE HONEY!!!