There's two problems that I see here: one, the whole rating system is terrible. It's capriciousness in determining what is - and what isn't - suitable for the screen is legendary. Mostly it has to do with how it's not a system that's suited for determining the merits of an individual film at all, but rather an arbitrary determinant of how controversial a movie is likely to be. I imagine that if Facing The Giants does have a lot of Christian sentiment, that alone would raise the eyebrows of the judging board. Clearly, some other system is needed.
Now, the second: these Christians, and too many of us do this also, are giving the rating system way too much importance. I know of some Christian parents who won't let their children see any movies with a rating over a G. Okay, well does that automatically qualify the movie for family viewing? I've seen plenty of PG-rated movies that should have been rated R, or at least PG-13. And one R-rated movie in recent memory, The Passion of the Christ, had a very powerful Christian element to it. I'm not saying that little kids should be allowed to see that, but there are certainly enough adolescents and up who could readily comprehend that movie... and maybe be affected by it in a positive way on some level. As it is, I know that some Christian pastors literally begged their congregations to "go see this R-rated movie!"
We as Christians are supposed to adhere to another measure than that imposed by the world around us. When we let something like a "PG rating" get under our skin, it's saying to the world that it has a power over us, when instead we are supposed to be free from its grasp.
Long story short: Christians should start thinking for themselves more, instead of letting others - like the Motion Picture Association of America - think for them.