Looks like you've chosen to buy a guitar then modify it by cutting the back off and chambering it. It's not a popular plan to mention to a buncha builders (obviously,hehe) but since this is what you have chosen here's some amateur's thoughts on your method...
*Like mentioned before, be careful how thick a slab you remove from the back so that you don't compromise the neck to body join.
*When you mention adding plywood to sandwich the body maybe it would make a more accurate cut by having the 2 plywood pieces slightly larger than the body (diameter) and completely squared up.
Then, as you're moving the sandwiched body through the saw you'll have a flat, square surface that might be less likely to tilt.
Also, make sure to use a fence so that the body doesn't shift side to side as you guide it through the blade.
*An obvious point but...be sure that while chambering the body from the back that you don't drill through the top (duh). A drill press or router set to the carefully measured depth is important and remember that the carve top will mean depth adjustments depending on where your chambering.
*I'd test the adhesive you use to attach the plywood to make sure it doesn't react with the finish or stick so well that the finish gets damaged when removing the plywood.
*There's a good chance that no matter how many precautions that you take, you may still get dents and dings in the body and finish.
*When you glue the new back on use lotsa clamps and cauls so you have a clean, tight join but again this is another chance that the clamps and cauls may damage the finish. Maybe cork sheets between the body and cauls may help to not damage the finish?
I'm a total amatuer so everything I've said may only sound good in words and not work at all.