When using a tripod, movement of water, leaves, clouds and the like are not always a problem, depending on the process used to blend the frames.
Even in the worst case (like shooting a beach with waves), you can usually pull it off by adjusting the blending via Layer Masks. I've managed even when stitching blended shots, for example doing 49 shots total in low light conditions with moving clouds (all for one 3:1 stitched pano).
The trick is to do gradual blends so the movement blends together cleanly.
If you are going to try the manual blending method be carefull about blending in areas that are fully over exposed in a given frame. If you do a partial blend there, you will get a gray look to your photo in that area. Even better, erase the overexposed highlights, before doing any blending.
I've had this whole process automated (photoshop scripts) for over a year now, and I have applied the technique to hundreds of images. However I develop after blending, unlike the method in the LL article.
Feel free to download the example4.psd file from this page,
http://www.farrarfocus.com/ffdd/examples.htmIt shows the resulting layers (with hand done layermasks to deal with the motion) for an image with large dynamic range and worst case beach waves.
Give the manual blending a try, with a little work you will get some great results!