First of all, I can buy that this is Brock's church. What I cannot buy is that Peter- as Spidey- went to the first church he could find with a high tower (he didn't know about what the bells would do in this story, unlike in the comics where Reed Richards told him sonic waves hurt the symbiote, so the only reason I can assume he went to the tower in the movie was because it was high up and seemed empty at that time of night) and it just so happened to be Eddie Brock's church, where Eddie Brock was downstairs in the middle of the night asking God to kill Parker. This is not one, but several coincidences!
And in the comics, by the way, Brock wasn't at the church. The Symbiote slinked off and FOUND Brock. So this version wasn't true to Venom's origin-- But then NONE of this was, and that's why I think Venom should never have been in the movie at all. I hate Venom, and just about everything else spawned from the Secret Wars (except maybe Arachne) and always thought he was a lazy, stupid, one-dimensional character, so his origin means nothing to me.
Doc Ock was robbing the biggest bank in town. Aunt May was at the biggest bank in town to get a loan. These things, while coincidence, make some sense. Eddie Brock wandering into a church into the middle of the night to pray for Peter's death is not a logical step for the character, didn't happen in the comics, and made no real sense. It was just a convenient way to get the costume onto him.
They should make a new cut without ANY Venom in it. I bet it would make a little more sense right away.