But I do believe Jiraya/Orochimaru would be able to fight pretty equal, and they are most likely stronger than Sasuke(Jiraya should have been able to protect himself against the Genjutsu in sage mide).
I do doubt though that Naruto will currently be able to kill Pain, as they haven't figured out his secret yet, and he's said to be impossible to beat until you figure it out.
Good points.
OK so let's start from the beginning and assume:
Orochimaru = Jiraiya = Tsunade
Jiraiya > Naruto 4 Kyuubi Tails (remember the training session? apparently he was able to defeat him without Yamato which is quite impressive. Maybe it is safe to say in this respect that Yamato + Kakashi = Jiraiya? Since they also had to control him while in this stage?)
Orochimaru also > Naruto 4 Kyuubi Tails
Sasuke > Normal Naruto (no Kyuubi tails)
HOWEVER:
Sasuke < Killer Bee Biju
Killer Bee Biju = Raikage?
This means that Killer Bee is stronger than Naruto, especially because Killer Bee can effectively turn full Biju and maintain his will where Naruto cannot. This means that Killer Bee is on the same level as a Sannin/Hokage or possibly stronger.
I think 2 Akatsuki = One Sannin because....
Jiraiya had to use a summon against Itachi and Kisame but did not use Sage mode. So possibly we can say Jiraiya is stronger than Itachi. (The cost for using sage mode is far less than the cost for using the Mangekyou Sharingan, so advantage Jiraiya) Remember too that Itachi could have beaten Sasuke if he wanted to. So this means that Jiraiya > Sasuke.
If Itachi were still alive I think he would be stronger than Sasuke and I think that Jiraiya in Sage Mode + The frog song from the elders would cancel out Itachi's Mangekyou Sharingan. So I think that the elder frogs were jumping the gun in saying that Naruto in sage mode surpassed Jiraiya. I think that they meant he was stronger than Jiraiya when he first was learning sage mode but I don't think he is stronger than the Jiraiya that just died. (I know you are dizzy after reading this paragraph, sorry

)
Another thing I completely forgot. Everyone has to remember that Sasuke effectively lost the battle against Killer Bee and had to run away. For some reason or another Killer Bee cannot be killed with Genjutsu alone even though supposedly the tailed beasts are weak against Genjutsu users, the Uchiha Sharingan in particular.
Now another loophole I think of is that Sasuke is weaker than Madara, However Madara cannot use Jutsu in front of Sasuke or the Amaterasu will activate. But let us assume they will not fight each other since they have the same objective.
As to your other point about Pein's secret...I think Tsunade mentioned the secret has been found out. At the end of one of the more recent chapters Pein for some reason assumed Tsunade decrypted the secret from the info gotten from the dead body examined by Shizune. She put Chakra in her hands and feet for some reason. Does this mean she knows the weakness of the Rinnegan?
Also@Beezer, yeah Tsunade is definitely a medical ninja first. But her power is equal to the other Sannin because she literally saved 99% of the villagers with the summoning jutsu slug (whatever her name is, i forgot). I think the slug can not only heal but absorb chakra attacks. I think it's only weak to Taijutsu which only one of pein's bodies use.
Overall I feel that Pein can be defeated if multiple high level nin are involved in the fight. Another problem is Sasuke and Madara wanting to destroy Konoha. It is already in ruins.
Did they mean the just village itself? I doubt it, I think they meant the people. Especially considering the concept of the "Will of Fire" that will continue to burn regardless if the village itself exists or not physically.