A lightsaber uses crystals to focus the blade, and gathering these crystals from the planet Ilum is a rite of passage for a Jedi. Under certain conditions, the crystals emit light and energy. Kryptonite is not typically crystalline; it's usually a metal or a rock. The crystalline versions of Kryptonite that have existed have emitted radiation, just like Green Kryptonite, rather than light or energy.
Kryptonite affects Superman because of its radioactive properties. Adding kryptonite would only make a lightsaber more deadly to him if the resulting weapon emitted the same radiation.
However, a lightsaber may be useful against Superman even without the presence of kryptonite, since magical weapons can harm him. If the Ilum crystals are by nature magical, then the blade might slice through Superman just like it can slice through Vader's arm.
You are blessed by the hand of your free chosen god