I have no problem with your complaint - it's a very valid one.

I just don't know how Ancestry would be able to make the determination outside of what the user inputs.
They provide the tools when you first enter info about someone (you have to choose living/deceased or enter info in the deceased field) and maybe they need the same thing when you upload a GEDCOM.

Or maybe make an easy way to indicate/flag that someone else has a living person showing on their tree. (although I can only imagine how this could be abused by a few).