Is there any way to forgo the autofocus points in my viewfinder? Perhaps replace the second piece of glass with a blank one?
You would need to replace the piece in question with another piece that is both the same thickness and has the same refractive index. You need the former so that the surface of the focusing screen remains equidistant from the lens as before (assuming it was properly adjusted before so that the light path from the lens to the focusing screen via the reflex mirror is the same distance as the light path from the lens to the imaging sensor when the mirror is moved up and out of the way). Differences in the latter might be correctable using the viewfinder's diopter adjustment wheel.
Note that the lights associated with the AF points would still be projected onto the focusing screen. The only thing you would eliminated are the outlines of the AF points that are visible even when the camera is turned off. The lights will always light up to show the selected AF point during AF point selection. They can be enabled or disabled to light up when AF is achieved via the Custom Function menu at C.Fn. III-3 Superimposed display.