What's the difference between natural honey and supermarket honey?
Both are natural honey - the difference is that commercial honey is often pasteurized to prevent growth of yeasts and the like. These growths are generally not nasty for you - it's how mead (alcoholic drink) is made, but honey can contain botulinum spores, which are bad for infants. 

Honey comes in two forms - creamed and liquid. The difference is that creamed has had some water removed and microcrystallization initiated to form a semi-solid. Liquid may or may not have had water removed and may crystallize if left for long enough in the cupboard.

There is no difference chemically between commercial and that straight from the beehive so no difference in GI.