First off, this may or may not of been listed but in all means I have not read this before. First off I will start by listing some facts then we will move onto the actual theory.
1. Itachi seemingly had no reason to kill the Uchiha Clan.
2. Jaraiya has(d) a "Reliable Informant" close to Akatsuki. Akatsuki moves bases.
3. The last time Jaraiya was in the Hidden Leaf before Naruto and so on was "Around the time of the Uchiha Incident"
4. Itachi read about the Mangekyou inside of a book in the Uchiha Hideout, also where Sasuke and Itachi are about to fight.
5. Jaraiya trapped Itachi and Kisame inside of his Stomach of Frog Technique. He did not harm either. Nor attempt to stop Sasuke from attacking him or prevent him from harm.
6. Itachi still has yet once proven to harm Sasuke. Always had used a Genjutsu.
7. During the Uchiha Incident Itachi spared Sasuke with no reason given.
Jaraiya's so called "Reliable Informant" is Itachi. The reason behind the destruction of the Uchiha Clan (Cursed Eye mind you) was due to the true nature of the Mangekyou Sharingan. Any user can resurrect through any Uchiha Member weaker then himself. Also why Itachi drove Sasuke to get the Mangekyou, or tried to.
Madara has not attacked Itachi as of yet due to not releasing the true information and also only having a Single Eye. Itachi did not kill Obito, Obito's body was saved due to Orochimaru of course (Orochimaru has always wanted a Sharingan eye). Obito was Taken over by Madara mid process, Madara having trouble was saved by Itachi due to Itachi also wanting to gain his trust.
Madara is out to destroy Konoha using the Kyuubi. Either Minato or Sarutobi gave Jaraiya instructions to Itachi. Also why Jaraiya was in Konoha near the Uchiha Incident. He told him about the book.
Does anybody find it the slightest bit odd that Itachi went straight into Konoha for no apparent reason? The kyuubi thing is a fraud due to the fact that they did not enter the Final Stage of their plan until after this. Meaning the true intention could possibly be to contact Jaraiya, which he did.