In my canon, different Jedi hold to different beliefs when it comes to theism; some are theists (monotheists, polytheists, pantheists, etc.) and some aren't.
In Ben's case, he's an agnostic theist -- ie. he believes in an intelligent higher power, but he doesn't know what that higher power is; it could be the Force or it could be something else entirely.
As for Nemec's comment, it's more a comment on religious conflict between lovers than on Ben's particular beliefs.