343 cannot unlink your MS account from Halo Waypoint since it is link to your Xbox Live account. I think the only way it can be unlinked is to change the email address and password associated with you gamertag/XBL account (although I cannot guarantee this 100%)
Hello Cats Like Yarn.
As Phil Mitchell62 has stated, 343i is unable to unlink your XB account from Waypoint. You can either try the above method or attempt to resolve the issue by contacting Xbox Support:
[/li]- Xbox Support on Twitter
I apologize that we cannot help you further.