Oh how the Akatsuki get's underestimated these days...What people don't seem to be understanding is that speed isn't everything. A crippled Edo Nagato was managing to restrain and hold down a KCM Naruto by himself, when Naruto had already become the fastest in the series.
There's also the fact that the more clones he uses, the shorter the time he can use them and there's the fact that since these clones are Shadow Clones, they'll disperse after one hit, and what do the Akatsuki happen to have ? Yes, a 360° attack that affects the whole battle field, the Shinra Tensei, which there is no escape from when they're fighting in a small cave. The Akatsuki are aware of just how powerful Naruto is, and would stick together and use teamwork to hold him back, with Pain being the MVP, since he has the perfect attack to take out clones, since, as I already said, they disperse after a single hit.
Then of course, there's the fact that since Pain is present, the Gedo Mazo is too. Overall, Nagato, along with his clones would be facing,
1. The 9-10 Akatsuki members (depending on whether Tobi is included or not)
2. Sasori's 100 hundred puppets (Along with his Human puppets which he might choose to take out instead)
3. Kakuzu's masks
4. The Gedo Mazo
This would without a doubt be able to overwhelm him. He's powerful, I'll give you that, but saying that he can take on the entire Akatsuki organization is outrageous.