Is it possible that the part he 'scooped out' was infected with thrush?
When we got our pony, she had bad feet that had only gotten rare, sporadic care for 3 years. Most of the ponies had feet that looked like elf shoes because they stuck out so far in front. She'd also been kept in a small paddock with several other ponies and had never been outside of that paddock. Her frogs were a mess. Our farrier showed me how to soak her feet before cleaning them so that I could work on them daily until they improved without hurting her good tissue. I was amazed at how much dead frog scrapped away after that first soak. Her frogs before and after looked completely different in shape and everything else. She was never sore after this was done though. She's got great feet now btw. =)
I'm inexperienced and agree that your horse shouldn't be sore afterwards...but I'm wondering if the farrier was trying to remove infected, dead flesh and went too deep?