In my opinion part of this is user error. There is nothing stopping anyone from disabling iMessage, or just disable it for your phone number and leave the email addresses attached to it.
I'm not quite sure how Apple technically should automatically and magically notice this.
I've switched three times (and gone back again) and never lost anything. The only times that I noticed I didn't get anything was when other users were actually messaging my iMessage linked email address instead of my phone number.
Granted the new website makes it easier to deregister for when you no longer have your iPhone, but lock-in it hardly was...