"it would seem strange from a UI point of view not to have a consistent navigation."
You hit the nail on the head, imagine is a website like Amazon removed the link on their logo to the homepage from the homepage, some people click this on the homepage just because they're confused and if they don't see a page refresh they may be upset. It's also a LOT more work to implement this.
I would argue a consistent navigation is good, as Google likes to follow a good structure, it's just causing you potential problems, what if you're using a CMS and you're on the blog, then you go to a blog article, do you remove the blog menu link as you're within the blog? There's just no real reason I can personally see for it.