That actually would have been somewhat amusing if Kisame swung his Samehada at Naruto only to find that it was a kawarimi created by Jiraiya as you see them both sprint away to the nearest room. Though we must not forget Itachi would win due to his exceptional skills in the art of run. xD
That gag was already pulled off when Naruto and Sakura first set out to find Sasuke in part two, and then it was Sai who finally found his room. Besides, if Naruto's team was that close it would have been very unlikely Hebi wcould have escaped. Clearly, Kishimoto wanted them to evade Konoha.