Generally speaking, yes, the water will eventually evaporate and the granite will get lighter. Now, if you had food stains (wine, berries, etc.), it's another matter entirely. (Random Internet advice that worked for me: making a slurry of flour and hydrogen peroxide, smearing it on, covering with plastic wrap, and leaving for a few days. Your mileage may vary, try in an out-of-the-way spot first, etc.)

I've tried a variety of granite sealants, and none have particularly prevented the very issue that you're seeing for yourself. If you can find better, I'd be quite curious.