So, there are souls, and then there are physical things. The souls are incorporeal, the corporeal things are physically there. If you are attempting to wrap your spirit weapons around the soul, you will have to treat them as a physical object with your weapon. If you treat them as a physical object with your weapon, they can treat your weapon as an physical object as well and pull back. Then as such, you will find resistance a possibility ergo, you may attempt to do this, yet since it isn't an assured way to render the souls out since it gives them a fighting change, you cannot say they are ripped out of the body in one post.
Hence not everything in hell is just a soul, those in the first layer are rendered without their bodies as their punishment, so their souls are without anything interact with the physical world. Hence, your weapons generally cannot affected them, nor they you as they are fighting on two very different states of being. Similarly, in such a line of logic, I question how your weapons at one point phased through the river of souls, and now at this point you claim they can wrap around the soul as if they were physically present...
The snake did get pulled out of the river however, which is good as it distracted it from attacking the boat since it was the only thing pretty much reacting to save your traveling vessel. Hence not all is lost. However expending souls doesn't give you a free pass to completely brush aside all obstacles. While there is indeed the brute force route, the easier route is to strike the weak points or analyze what's wrong with the scenario given.
Since this is the first battle, I'm going to reveal the design of this challenge and leave it you folks to see if your characters can logically deduce this 'key' to solving the snake:
1. As mentioned, the spirits cannot directly interact with the physical world, save for speaking their thoughts and attempt to sway your minds.
2. The snake is dead, yet somehow the spirits are able to possess the corpse and use it.
3. Something is animating the snake, which is how the spirits can control and manipulate the snake through their will, as such exists some form of spiritual conduit they are stored in.
4. Snake shed its old skin for a new hide, becoming more difficult to penetrate its hide due to the scales which become more resistant to what strikes it with each molt, Uxzan's arrow however manage to slip by scales from its small size and penetrate it, embedding it within the snake.
5. The old skin of the snake is not animating itself, hence it cannot be the part which harbors the spirits.
6. The snake is dead, yet someone in the past has managed to kill it, and not only this, but cut it into three parts which should be impossible due to the nature of the beast's scaly hide.
7. Stabbing the brain did nothing to stop them, the blood is rotting itself so the heart is probably also useless.
8. The snake speaks, but speech is not a function intrinsic to the snake (usually snakes don't speak, particularly dead ones), however that being said it is not the snake speaking but rather the voice of the spirits.
9. The internal organs of the beast are well protected from attack by its skins defense, although none of them really would matter. However some organs are not as well protected such as the eyes or tongue. But these are not usually attack targets, as what good is piercing the eyes of something without vision?
10. Hence how can the snake see? The spirits have to be possessing something which allows them to detect the movements of everything else, since the brain isn't integrating anything.
11. Tongue. The sensory organ which allows the snake to detect chemical changes and more importantly, speak.
12. The spirits are controlling the snake by channeling themselves within the beast's tongue. Sever it to silence them.
13. Alternatively, if you can tear the corpse to ribbons by attacking where the skin is weakest, from the inside. As the original hero did, by letting the beast consume them as they cut their way out of the snake since its scales cannot protect it from internal damage.
