We've been aware of this for some time now and only buy from a local small apiary. We try to avoid HFCS in as many food items as we possibly can. It is awful stuff in every way.
We still intend to do our own bees by the top bar method. We want to leave the honey for the bees through the winter and harvest in the spring. From there, we should be able to learn how much we can take and how much we have to leave to sustain the bees through the next winter. This way we don't have to give them a syrup or sugar syrup (which can often be HFCS) to sustain them artificially until the flowers are out or during no-flower times and we can keep it out of our final product. Doing this won't make us a lot of money, since we are not stripping all of the honey out of the hives before winter, but it will be much healthier for the bees.
Did you know that you can find some of the HFCS/sugar syrup (and its contaminants) in the first honey run and in the honey throughout the life of the hive? You can also find contaminants in the wax that remains as well. We found that interesting, and since we want our honey to BE honey and not something else, we figure that doing bees ourselves and by excluding what contaminants we can control, is our best solution. It is just too bad that we can't do it fully natural/organic. We figured that there really is only a very small area in Canada where this might even be possible, and it was pretty remote. I really hate seeing honey marketed as "Organic honey" when you know that according to regulations, it really cannot be.
Unless all weed districts stopped spraying and all the farmers quit doing the same (which will never happen), or the bees learn to stay within certain boundaries, that just cannot happen.
As far as the allergies...what I have read is that if the honey is very local, it will contain local pollens, and therefore should help alleviate allergies. If it is from farther away, it contains different pollens and so cannot help.