This isn't a laptop, where half the cost of the device comes from a single part. It's a lens. You'd expect repairs to never cost more than a quarter the cost of the hardware. If they do, you're getting screwed, and you're better off parting it out and selling the pieces on eBay for twice what it costs to buy a replacement lens. It takes longer, but if you're seeing five hundred bucks for a lens repair, there's some massive pocket padding going on there.
No matter what, a repair shouldn't take three hours of a technician's time. if the lens really took that much time to calibrate, it would cost a lot more than that to sell it to begin with. I'd expect Canon to just replace an entire lens group, then send back the pieces for remanufacturing, where the parts of the lens group get put back together and calibrated in an automated fashion, just like they do during manufacturing. This leaves just a handful of calibration adjustments that technicians actually make during most servicing. I could be wrong. If I am, then Canon needs to rethink their service procedures.