Discuss it with your dealer. Some are understanding and some are pricks. Every car I buy gets modified. On my current daily driver ('07 Mustang) I replaced the entire suspension - i.e. springs, dampers, sway bars, wheels/tires, brakes and a bunch of other things including a twin screw roots-type blower running 15 lbs. of boost. I had very few problems during the warranty, but never once did the dealer refuse to repair it. They did try with a faulty brake pressure switch, but the upgraded brakes I installed were OEM from another model. I explained that both models use the same pressure switch so they agreed to repair it.
As I mentioned previously, a lot of dealers recognize that there's a fair number of enthusiasts who like to personalize their cars. A simple spring swap isn't a very drastic mod. It's also not likely to affect the ride all that much. The choice of dampers has far more of an impact on ride (no pun intended).