I'm looking into this further, but the test project has no such issue. When equipped with only one two handed weapon, there is no extra attack, with or without the barehanded attack option enabled.
Are you also using the monkeygrip extension? The extension might be overwriting some of the changes I just made. Also, if the actor we're talking about has monkeygripping enabled, the two handed weapon in the main hand would be considered a one handed weapon, meaning he should be able to get a barehanded attack as an offhand attack, at least if that parameter was enabled.
~Ramza