The key to understanding "Hallelujah brother, pass the mustard" can be found several lines earlier in the scene when Edward says "Carter, we've all had hundreds of these discussions......and every one of them always hits the same wall. Is there a sugarplum fairy or not? And nobody has ever gotten over that wall."
Throughout the film, the two protagonists often bring up their differences about the existence of a higher being.
"Hallelujah brother, pass the mustard" is Edward's way of saying (once again) let's agree to disagree; I respect your opinion but, please, let's move on and just enjoy the view.