First and foremost this is NOT an insult to any people who are pagans. This phrase plays off of misconceptions that people have who view pagans as very mystical and spacey.
The phrase "fucking pagan" can be used with a person (often times women) who are just completely stuck on silly romantic cliches and won't let them go. Examples of these cliches include the feeling that the eyes are the "gateway to one's soul" and that there is only one true love in the world for each person. You would tell a person who is insisting on something like this that they are being a fucking pagan.
The phrase was originally derived from Million Dollar Baby (Clint Eastwood's priest).
-Girlfriend: "What part about me do you find most attractive"
-Boyfriend: "Uh... well to be quite honest I think that would be your ass"
-Girlfriend: "You're an asshole, you are supposed to say something sweet like my eyes, they are the windows to the soul"
-Boyfriend: "Can you stop being a fucking pagan for a second? Eyes are all the god damn same. There are a few differen't colors and thats about it. They aren't magic jewels, they are eyeballs."
*Girlfriend storms out, no lesson is learned*