trouble after shaving civic drip rails

I have a 1980 honda civic hatch. I have some rust on the roof near the drip rails and was wondering if i shaved them would I have a problem down the road with the metal work or bodyfiller cracking from flexing. I'm not baggin the car but i am gonna have coilovers on it and slammed with a 98ish sohc vtec fuelinjected swap in it.Is there an easy way to do this or should i just ride out and not worry with it. thanks