they seem to be a relic of the pre-Lord of the Rings conception of the story, i.e., not intended to be in continuity with the Silmarillion.
Several such concepts -- goblins rather than orcs, talking trolls, skinchangers, dwarves (!), sentient eagles, and the Council's apparently relaxed attitude toward Dol Guldur were extensively rethought and incorporated into the larger mythology. Stone giants weren't.
This leaves a problem when one is retelling The Hobbit specifically to incorporate it into the Lord of the Rings. One can solve it in three ways.
1) Omit the stone giants. They have no impact on the plot.
2) Render them merely as cave trolls -- "stone giant" makes perfect sense as a folk-name for cave trolls, after all, and stresses the difference between the two types of trolls encountered. Bilbo was exaggerating their size and strength a bit to make the point.
3) Depict it as an exaggeration or outright lie -- a fanciful addition to embody the thunderstorm. Bilbo is not a completely reliable narrator, after all. This could've been done with a neat cutaway to Elijah Wood, or, in my preferred version of this movie, to those hobbit kids Bilbo was entertaining at his birthday party back in Fellowship. Bilbo could've even indignantly defended himself.
What one cannot do to solve the problem is to introduce a race of titanic beings never encountered by anyone other than Bilbo et al. But, hey, I'm sure it'll be a cool level in Lego The Hobbit.