Microsoft's solution above is tacked-on and inelegant, it's a bandaid to fix a problem with WMDRM that MTP devices were causing in the first place. MTP wasn't built for enforcing DRM and and Amazon would just be setting themselves up to face the same issues if that was their goal here. Also, unlike Microsoft, they don't have the advantage of being the original creators of MTP. If they did want a completely DRM controlled environment, turning the Kindle PC app into something more like iTunes where it's the only program able to communicate with Kindles would have been a much better first step than implementing an industry standard file transfer protocol. They could have jumped straight to your second step like that.

My best guess as to why they're making the switch to MTP is because USB Mass Storage currently requires them to maintain a separate partition with a fixed size formatted in ~~NTFS~~ FAT32 on a Linux-based device just so it can occasionally be exposed to a PC it's plugged into, and that's... kinda stupid. MTP provides them the option to just not do all that. MTP is the standard mobile devices use these days, it's going to be easier and cheaper for them to develop around and they won't need two different file systems and partitions on one device anymore.