Not quite sure exactly what type of lenses you are talking about, but I think you are referring to the lenses that are made to "shape the cornea" and not the ones used during the day for distance vision.
I actually don't know the Academy answer to your question; however, if he can put them in and get them out on his own time then nobody will really care what he does. With that being said the mornings are usually very quickly paced, as in you wake to the playing of reveille and within a few moments are standing at attention in the hallway. There really isn't time to do much, especially get contacts out or in and in the correct solution.
I would recommend wearing glasses for Indoc unless you are wearing the extended wear lenses that you keep in for a week or two or a month and don't take out on a daily basis. If you do wear that type of lens you could probably do it; however, I would never recommend sleeping in contact lenses as that can bring about all sorts of problems. I would say 90% of the corneal ulcers I've ever seen are in patients who have slept in their contacts.