As you see it you have two main options: either integrating the nacelles partly into the saucer section, which will shield them from battle damage; or outriders off the edge of the primary hull.
For the protected variant you would have to clear the outer edges of the saucer, really pushing space to a premium in the interior. For a dedicated combat ship that seems entirely practical, and you know the Defiant Project is pursuing a similar strategy. The loss in efficiency will drive the practical range of the ship down, though. The outrider nacelles on the other hand would increase the ship's profile and present an obvious target. The Borg would probably blow through regardless, but you're thinking more of standard engagements.
With arguments being made in favour of both you turn to the main deflector as the deciding factor. The standard deflector design would serve here, but in that case you really would have to use outrider nacelles to get decent performance out of the warp drive. On the other hand a new design is being proposed that would use an antiproton-charged dish to enhance the deflector field. If you could use that then you can offset the unacceptable performance losses from the internal nacelles.
The Internal Nacelles are not only better protected they also minimize the profile of the ship and the Antiproton Dish allows to compensate their bad range/endurance:
The outriders increase profile, are a gigantic shoot me there sign and their only advantage is more internal space! Somehow I do not think that fucking labs, Diplomatic lounges or anything non combat related will save a warship once an outrider nacelle was blown away on the first hit.