"grants a user access to a part of my website without going first to my site's home page, the user may experience something different from what I intended when I established my website"
Rather than fight technology -- particularly when it's in the user's interest -- why not adapt?
There's already a marketing obligation to optimize every page on a Web site for search engines.
And there are a proliferation of other routes by which users can arrive at any page.
Is it so unfair (not to mention the pragmatism) to optimize for users also?