My feet get calluses on them too, but if I wear shoes and socks rather than flipflops, the calluses remain supple and easier to deal with. I get a PED egg and using those tools, I file them down rather than pick at them. The PED egg has two surfaces for calluses, one a bit like a cheese grater and the other like sand paper. If your calluses are extremely thick you could start with the cheese grater and finish with the sand paper. http://www.amazon.com/Pedicure-Foot-File-Colors-vary/dp/B00113FENI
There is also a product called NEW skin.
http://www.newskinproducts.com/products/liquid_bandage.aspx
Although it doesn’t say on this website, it says on my bottle that you can remove a callus and use it to help prevent future callus formation. I have also picked my calluses and experienced the same pain you do. New Skin fixes that problem. (Yaay!)
One caution, if you have any sort of infection, NEVER use New Skin. It will seal it in. New Skin has lots of clove in it, so although it stings a bit if you apply it to a raw wound, it relieves pain once it cures.