During Itachi Nagato vs Naruto in episode 298. We have seen Itachi's decision been changed by kotoamatsukami. Kabuto also noticed this. Why didnt he just closed his reanimation and close him in the wooden closet?
One of the reasons can be, as Madara had mentioned, the summoning through reanimation jutsu is a two-way contract. Even if the caster wants to, he may not be able to un-summon (as was seen with Madara). Another reason can be that Kabuto didn't really care about the war. He just wanted the "game" to go on. He wanted to collect as much information as he could, and Itachi breaking free of the jutsu was really something that was unseen and Kabuto just wanted to see more.