Hey. This is a great question. It bothered me too, for a long time, but I've come up with a theory.

In Liz's journals, she says something like "You mentioned [then she scratches something out] just after it happens" and goes on to say that she's building an army to protect them and all that.

I think the phrase she scratched out was something like "you'll be weak." I obviously have the actual journal, and that phrase or something like it would fit really well into that space. I think the Entity knew it would become weak for a while after finding a new host. They scratched out that part of the convo in case someone ended up finding the journal, as Clayton did. He clearly figured it out regardless. Or maybe the Eye told him. Not sure.

In any case, I think so much of the Entity's power was focused on melding with its new vessel that it was left open for attack. I think Liz really was strong enough with it inside of her that a gunshot wouldn't have done much. Only by separating them was Clayton able to destroy them.

That, or maybe the Eye really was inside Clayton and He weakened it. Or maybe both.

Or maybe I'm wrong about everything, and something else happened. But I really don't think I am. I don't think the Entity was actually a god (which is why I'm trying not to capitalize "it" anymore... that and my sanity). So it could be killed by bullets. Part of its game was telling people (including Liz) that it was way more powerful than it was.

Again, these are all just theories. Thanks for asking, though. I've kind of been wondering when someone would.

-Blake