I haven't been playing the game long (54 hours and counting), and I haven't seen any discussions so far, so forgive me if this was already discussed.
I'm guessing there's lots that have thought of this, but what if Telamon's disappearance is why the Atlas lost control of the Sentinels? We know that Sentinels are the Atlas's security force (I say security force because in this sense I'm translating the word 'police' used in the wiki to what I believe it's equivalent would be in a computer/simulation), and Telamon was the security sub-protocol for the Atlas. What if Telamon also handled the Sentinels? If that is the case, then Telamon's expulsion would mean Atlas has little or no control over the sentinels anymore, which would make sense.
Now I haven't crawled through every corner of this wiki yet, so I'm not sure if it's discovered or discussed by anyone what exactly went wrong with the Atlas. This is just a theory of mine that I wanted to explore with others. If anyone has proof that the theory is incorrect I'll be eager to see it, as well as any evidence that it is proven true.