My guess is that Kisame transformed into the girl. I also think that Jiraiya knew this, because he told Naruto to go into the room and mold chakra. Now, this is just a guess, but maybe he wants Naruto to do this because either:
A) Use up all his chakra so he goes Kuuybi on Itachi.
B) Get ready to fight so he can see what Naruto can do.
C) Just because he was blind at the time and just wanted to hang with the girl.
If the answer is C, then I'm guessing he's going to see the REAL version of the girl, then kick the fakes ass (if it is Kisame or something).
Also, did anyone notice that when Jiraiya and Naruto regiester at the inn, the girl with the green hat is behind the counter (the same one that Sasuke talks to)? Maybe Sasuke is in the same hotel as Naruto and Itachi after all.