You are dead right. You need to brace the body by welding temporary braces diagonally across the doors and the body. Because you dont have a chassis rig (car-0-liner pull bench etc ) this is the only way you will prevent the car from distorting hen you remove the rusty bits. I just use scrap for this part and i measure,measure and measure again. You should also get the car up on solid stands so that it's not sitting on it's springs . The body needs to be as solidly mounted as you can get it.
If it is on it's springs you will distort the body once you remove the sill section and this will appear as a wavy roof and/or the doors and screens wont fit properly.