When Gary Kerr was researching for Round2/Polar Lights' 1/350 scale TOS Enterprise
model kit he learned that you can get such a hangar deck into the ship. McGagen
(who posts on Hobbytalk) has built a 3D Enterprise
with a MJ hangar exactly where it's supposed to be. His work is outstanding, too.
It will fit in a 947ft. ship, but it's a close fit. A 1080ft. ship would give you a bit more room to play with. Matt Jefferies had a pretty damned good idea of what he was doing.