Why would a Christian want to kill the antichrist?
Does everyone in the show think that God is totally incompetent and has really poor planning skills?
The antichrist is the key figure in starting the apocalypse, which is when Jesus returns.
What do these Catholic priests think will happen if they succeed in killing the antichrist?
The omniscient God says, "Oops, didn't see that one coming. I guess Jesus can't return to Earth, all the Biblical prophesies are invalid, and the universe will have to just continue running along without me. It's too bad I make all my long term plans with a single point of failure over which my omnipotence somehow has no control."
Why would anyone other than a Satanist want to obstruct God's plan?
All those people helping Damien must be among the most faithful Christians on the planet, so why do they always get such ominous music?
Maybe the writers are cleverly pointing out how the God of the Bible is clearly the bad guy, and Satan is the plucky underdog with really bad press. It's too bad for the devil that the only book that describes him was written by his mortal enemy. What if the only historical source for Jewish history was written by Hitler?