I use honey
instead of sugar. The bee pollen is only a very small amount. It's kinda like adding vitamins. Most of the carbohydrates (apart from the small amount of honey
the bees mix in) in pollen are bound up in complex, non-fermentable structures. It's very high in protein, minerals and vitamins. Besides, at the typical going rate of $1/oz, you'd have some pretty expensive ginger beer. And adding the pollen is really just something extra...it doesn't necessarily add much to the flavor or character (unless you use a lot, which is not advised - see previous post on shutting down the ferment).
You could always put your ginger beer under an airlock and let it ferment out completely so there's very little or no sugar left. But ginger beer is generally intended to be like a natural soft drink - usually it's only fermented long enough to carbonate bottles and retain a fairly high amount of residual sugar. For most people it's supposed to be fizzy and sweet.
There is another type of ferment few people seem to be familiar with, which is making your own bee bread instead of taking it from the hive. This is done by mixing pollen, honey
and water, and allowing it to lactoferment. http://www.fao.org/docrep/w0076E/w0076e11.htm#3.12.2
You should keep in mind though that bee pollen is EXTREMELY nutrient-dense, and some people experience some gastrointestinal distress if they consume too much. You have to start small and slow when consuming bee pollen, like 1-2 teaspoons per day. And some people have been known to have an allergic reaction to eating bee pollen.