jiml8 and Micro420 both suggested that maybe there's nothing wrong with your disk, it's SMART that's at fault. If you think they're right, and the SMART messages are annoying you, then just disable SMART.
But if you still want to run fsck then backup your data, and just go ahead and run it at the next boot.
My system is set to run fsck every 30 boots. If your filesystem is broken, or inconsistent, then continuing to use it without running fsck is only going to make matters worse, so don't be too worried about the "scary message": Bite the bullet or ignore the "problem".