ThisGenin or not, Naruto at that point had just defeated Sabaku no Gaara and Shukaku, who was actually the strongest Suna shinobi and had been unbeaten or even hurt up to that point. Furthermore, Kisame was relying on Itachi's intel about the kyubi jinchuuriki since Itachi was the one from Konoha, and Itachi was feeding him garbage because we all know why, he's a loyal Konoha shinobi. Also, when refering to Jiraiya, notice that Kisame and Itachi compare the TITLES between them and Jiraiya, that the title of SANNIN eclipses that of UCHIHA and SEVEN NINJA SWORDSMEN, in other words, it could have been Tsunade or Orochimaru in Jiraiya's place and the conversation would have been exactly the same. This scene in NO WAY whatsoever proves that Jiraiya>Itachi Kisame or even individually in battle. Only the most die hard Jiraiya fanboys would think other wise, ESPECIALLY after Tobi told us the truth about Itachi.
+ in some translations Kisame doesn't even say that they pale compared to a sannin. In the translation on NB's manga he says they are a good match up for a sannin.
Also Itachi one shot Orochimaru,another sannin.