Thank you Madness. Good to see you as well.
The things to remember:
1) The Scarlet Spires had already wasted their strength blasting into Shimeh while the Fanim conserved theirs. It's bad enough that one of the senior magi begs Eli to stop and he laughs it off and continues to push. I'm going to repeat that because it's important: the Scarlet Spires continues to push after one of their senior magi warns their leader that they are squandering their strength and this is before they fight a single Cishaurum. The Scarlet Spires throw away one of their only advantages before the fight even begins.
2) The Cishaurim don't just ambush them. The encircle them and unleash their Chorae archers as well. Envelopement is pretty damned deadly and the Spires shield men can provide only limited protection. The Scarlet Spires tire themselves out in the process of walking into a trap where a fresh enemy waits to spring upon them and Chorae archers can attack on all sides. It isn't strength that wins this fight for the Cishaurum (although they clearly have a fair amount of that as well), it's tactics.
3) It's not an impressive display of strength to overwhelm exhausted men. Despite this, Eli is able to hold off two of the greatest Primaries and some of the Scarlet Spires survive long enough for the Men of the Tusk arrive and provide some aid.
4) Despite having wasted his strength, despite having two of the strongest Primaries gang up on him, Eli is able to fight on until finally the strongest of Cishaurum overcomes him. You're not proving yourself stronger than a guy you don't fight until he's tired, gang up on, and then manage to beat when your buddy who was helping you drops out of the fight. You are, however, stacking the deck in your favor.
5) No one is saying the greatest Primaries aren't really powerful or greater than many Anagogic Schoolmen, but nothing indicates that the Cishaurum as a whole are more powerful. If they were there is no way Eli could hold out against two of the greatest Primaries after wasting so much of his strength and he's not only able to hold out, but to counter attack and fight on against their strongest when he's given a little respite by having one of those Primaries who is beating the shit out of his wards fall. Eli's feat of endurance is exhausting in of itself. When I was first reading the Thousandfold Thought I was thinking "Christ, all this and they still haven't managed to kill him. Is he somehow going to live through this shit because this is hardcore?" And just when I think he might actually Rasputin his way through his fuck up (and it's a colossal fuck up, he leads his entire School into a meatgrinder) he finally is beaten down and dies.
There's also the small matter of having seen powerful sorcerers swiftly overwhelm weaker rivals and hold out against superior numbers of weaker enemies and Eli's performance is consistent with great strength. It takes a long time for him to fall and a lot of hammering just as it takes a massive beatdown to overwhelm Akka. The mercenary mage, on the other hand, doesn't last long against Eli. That does show there's a fairly significant variation in strength between Sorcerers of Rank, consistent with having the strongest Primaries being able to outmatch many Anagogic Sorcerers one on one, but it's also shows just how strong Eli by being able to hold out against two Primaries even after squandering so much power.
5) Kelhus choses a highly mobile strategy to fight the last remaining Primaries and their supporting Chorae archers. His ability to teleport and his lethalness in close quarters is an advantage only he possesses. If he allows them to concentrate against him they might kill him. If, on the other hand, he's teleporting around he's a hard target to concentrate against and he can attack his opponents by surprise. His telekinetic rubble shield also helps protect him from Chorae archers but why would he do them of the favor of staying still and lining up shots?
This is another example of Kelhus's intellect allowing him to make full use of his abilities.