I don't want it so freely used either. I like how in the comics it was something slowly discovered, Superman was unsure what was happening to him. And when he did find out he became very concerned. It's got to be used sparingly and be (dramatically) built up again.
I wouldn't want it as a major plot point right away. It's more effective the longer Superman is built up as invulnerable. Then the kryptonite appears. At this point, it just seems too convenient and cliche.