I think Naughton will cope fine in open play, but adding a player or two that can really challenge in the air for the set plays can make a real difference in games like these imo. Much tougher for Stoke to build pressure by winning set piece after set piece when we have a few players in addition to the centre halves that can really put up a fight for those long throws and set pieces.
Dawson, Caulker, Vertonghen, Sandro, Dembele as well as Dempsey and Ade (if fit), Walker is reasonably good in the air too and we should be able to deal with whatever Stoke (literally) throw our way.
Add to that Sandro (and Dembele) who can challenge for the first header after their long hoofs from the goalie leaving our centre backs in position to deal with whatever happens after that first duel in the air and I would be feeling quite confident. Normally Stoke will sit back away from home and I would imagine they will do that against, the only real issue will be how to unlock their back 10 or whatever it will be.