Yeah, if its not an injury, keep doing 'em. The cramping probably means your muscles have no idea what you are doing to them, which is a good thing. Do lighter weight and keep doing em. Your hammies will thank you later. Oh yeah, do you do walking lunges or the stationary barbell version? Try and mix it up and see what feels better.
Are you doing them with weights? If so, stop. Really get the form down, taking a long, deep stride and moving dynamically (not lunge-rest-rest-rest-lunge; but lunge-lunge-lunge). A few weeks from now, when this is easy and you no longer are crazy sore the next day after 5-6 sets, begin using some weights.