> How can the pantry beetles be eliminated without applying 
> something that would harm the bees in the future?

Beetles can't be frozen easily, many have "antifreeze" in their "blood".
Heat won't kill them either, you'll melt the combs before you kill the beetles.
CO2 would kill them, but it is hard to seal a room tight enough to keep the CO2 levels high enough long enough.

I'd take the whole mess down to Sterigenics Corp in Salem, NJ, who has a track record dealing with bee boxes, and have the beam power settings worked out to get all the way through full boxes of comb, and leave a "sterile" result.  If you just want to kill beetles, they might be able to turn down the power a bit, as they usual need is to kill AFB, which is a tall order, even for a Cobalt-60 source (gamma radiation).

The result is clean, no residue, and (of course) no residual radiation.  As I remember, their price was under $200 per 6-foot high pallet. 
This works out to 6 stacks of supers, each under 6' feet higher per pallet (you can trust me, my Pallet-Fu is strong, as I am constantly shipping pallets of Bee-Quick hither and yon).

It will be some work to properly prepare the pallet(s), you have to wrap the pallets in plastic pallet-wrap, and line up the stacks of supers properly, and follow other rules... there was a write up that floated around a few years ago from the MD beekeepers on how to do all the prep, but the company likely will send you their own cheat-sheet.

The wear and tear issue on the boxes is minor, but it is there - no doubt at all that gamma rays will also break cellulose fibers in the wood, and that means more moisture absorption is possible than in non-irradiated wood.  But it is the wax combs that are being saved here, so I would not worry so much about a minor degradation of the boxes.  Well-kept honey super combs always outlast their boxes.

Disclaimer: yes "Dr. Bruce Banner, pelted by gamma rays, turned into the Hulk" (https://youtu.be/b9u7GjNkp5Y)  but you won't be anywhere near the beam when they light it up.

See?  Physics IS useful in beekeeping!

             ***********************************************
The BEE-L mailing list is powered by L-Soft's renowned
LISTSERV(R) list management software.  For more information, go to:
http://www.lsoft.com/LISTSERV-powered.html