From the conversation between Kellhus and the Mutilated, it seems the Gods can see him just fine. They just can't see where he stands. I agree that this is the weakest part of my theory, though.
The Mutilated explicitly state that Ajokli HIDES from the gods in the Golden Room. I'm fairly convinced that while the gods obviously saw and were aware of Kellhus up to him entering Golgotterath, he was utterly invisible to them once he entered it. That's why Ajokli had to ride along inside a Decapitant.
But here's something to think about. The Consult are not content to just sit in Golgotterath until they die. Which implies that merely being there doesn't completely hide you from the Gods, at least after you've died. So I'm pretty sure Yatwer knows that Kellhus dies in there, even if she can't see the events that immediately surround it.
The concealment offered by Golgotterath seems to be purely in the Inward. Once you die your soul goes to the Outside, so even the immortal members of the Consult would still be motivated to fire up the No-God. Wait around long enough and eventually somebody might show up who's powerful enough to kill you, and then off you to go the Pit. Yatwer would know Kellhus died if his soul turned up in the Pit, but that seems unlikely unless she snaffled it up and is capable of hiding that from Ajokli. That's plausible, Yatwer IS powerful, but why would she hide the fact she held Kellhus' soul from Ajokli?
To Yatwer, the only visible souls/agencies involved with Kellhus' death are Sorweel and Esmenet. They both intended death to Kellhus, and Kellhus died in proximity to them, and with no other souls/agencies around that Yatwer could perceive. Hence she intuits (because she cannot reason) that they killed him. She sees the outcome and the intentions, and fills in the missing details of the causal chain in an intuitive and rather dim manner.
I don't see any contradiction between your argument and Yatwer seeing a Skin-Spy killing Kellhus, assuming of course she could see what happened in the Golden Room at all. To Yatwer, the actions of the Skin Spy Employee of the Month were the culmination of a causal chain that all happened in accordance with her plan. Sorweel died to place Kelmomas in a position to ultimately be in the Golden Room. Esmenet actions served a similar function.