That does sound like a pretty good solution, if it can be done for a broken phone. The major issue I see is that refurbish companies are already complaining about "bricked" MacBooks, because nobody actually cared enough to ensure that those laptops where reset before being sold. I don't see the same industry being capable of guiding users through resetting permissions for spare parts.
A better solutions is to take the direction FairPhone has chosen and make the things that break user-serviceable and offer the parts for sale on Apples own website. If the issue is that phones are being stolen and sold for parts, just flood the market with cheap parts. The new iPhones are absolutely massive, so I'm not buying that you can't make them a bit thicker and allow a user to take them apart. How many people use their phone without a cover anyway?
If Apple is serious about being more environmentally friendly, then make a user serviceable phone. Not replacing your phone because fixing it is either impossible or impossibly expensive is going to have a much bigger impact than buying carbon credits for people who charge their watch. My best guess is that Apple is so obsessed with just-in-time production and so hostile to the idea of stocking parts, that they can even see the potential benefits.