A quick interpretation (spoilers)
This was quite a good movie. Here's what I got from it... The movie is about Jesus and his Second Coming. Just one way that the event can pan out...
I think there was a rapture-type event going on.
The entity at the bottom of the sea looked liked a giant anus.
Just think about it: Anus = asshole = a soul = a Sol = a sun = The Son of God
So, yea, something that on the surface looks truly horrific is actually the most benign thing ever. The coming of the son of God. His taking all the faithful into the next world with Him.
That's just an interpretation... What did you think the movie was trying to communicate?