I really can't see what shooting the lower pressure black powder rounds could do to your Krag if you clean the rifle well after shooting. But, I have never seen any loads documented in black powder for the Krag. It's taking a step backwards since the Krag was developed around the smokeless powder.

Buy a nice condition trap door and shoot it with black powder. It's a neat experience. I had to buy a nice condition trap door to have as a nice Springfield Armory creation that immediately pre-dated the Krag to see so many similarities in design. There are many out there at affordable prices. Then you can shoot the Krag and trap door at the same setting and enjoy history!