I DID read the story. The only way that there could be $1000 difference between what was taken in and recorded on Sunday am and what was deposited is that SHE was making the deposits. That is not enough separation of duties.
The bookkeeper should never touch the money, at least not at a church. Also, another person should have been going over the check register and bills. Purchase orders help. It was not the only way she was cheating obviously.
I agree with your comments about deposit controls and controls in general
They caught because of the deposit theft which means they have some controls in place.
Unfortunately churches are too trusting thinking everyone who works for them is honest. And second this person was a bad actor from the get go