Do you have any idea what’s envolved with changing a Shimano freehub? assuming you mean the freehub body & not the complete freehub?
You have to dismantle the hub to do it, so axel & bearings out, remove old freehub body, (which is probably siezed if original after 3 years)clean, fit new freehub body. What would you like then? dirty gritty bearings fitting without any fresh grease in your new freehub body, or cleaning & fresh grease to makre sure it runs properly?
Yes they probably should’ve called you if it was going to cost more than you expected, but at least they did it poperly!