The idea is good, but a little hard if you will put more than one person, since the class can get only one student before the Mundus magicus arc, or two after, but that only making the assumption that all of them will come back (and would need a lot of imagination an planing to make a story of what happened after that, and make justice of the original story) :unsure: .
If my memory don't fail me, there was a dodgeball game on the first arcs where the class challenging negi's class wanted him to be their theacher. Meybe if the game anded in a tie(don't ask me how :sweat: ) he would need give lessons on both 2-A and the onther one(that one baing as troublesome as the other). Maybe not since he coul be overloaded that way. <_<
Naruto acting like a girl could be interesting, meybe in an undercover mission or a test (like the one negi passing trought) to rise in the ninja ranks, so he need maintain the disguise and get some information of the magical part of Mahora, but end involved in all the mess Negi caused.
Index Libroriun Proibitiun, or only index(from To Aru Majutsu no Index), with Negi trying to help with the fact that people try to kindnap her every week because of the god-know-how-many books on her head have potential both for crack or serious stories.
Edit: The other class was a senior one (2-D if Im not mistaken), there were shown only about 13 of them there, what give possibilities of a LOT of "troublesome students" to the young teacher.