Without inspecting them, you would not know what you would be losing by blindly resolving to removal, hence we do not auto-resolve "one side removed, the other side changed" to a removal.
That does not need to mean that we should not make it easier for the user to say "resolve these 'one side removed, the other side changed' paths to removal".
"add -u" will be a way to say "Record the changes I made to my working tree files to the index". So presumably
rm -f those files that the other branch removed
git add -u
would be one way to do so. Of course, you can also use "git rm" directly, i.e. git rm -f those files that the other branch removed