I'm always up for learning something new. Below is a recent pic taken with a 2 stop grad ND (3 stop would have been ideal). The ND was rotated at an angle consistent with the sun/shadow line. I'm not sure how you would shoot different shutter speeds and layer as I would think the water would appear inconsistent. However, if there would be a way, I would like to know as it would be another tool to use.
If I were doing this and I wanted to properly expose everything without filters, I would bracket the exposures at about F11. -2, 0, and +2. Or if you are using Magic Lantern, 5 exposures at -2, -1, 0, +1, +2. But honestly, 3 exposures should be fine. I would then figure out if my shutterspeed was slow enough to smear the waterfall within one of these exposures. If not, I'd experiment with raising aperture from F11 to whatever aperture I needed to slow the shutter and smear the waterfall. The only thing moving in this photo will be the waterfall as long as the trees are not being blown around a lot, so your shutterspeed can be whatever you want it to be to get the waterfall as you want it.
One of these aperture settings should give the effect that you need with a properly smeared waterfall. If so, I would go into Photomatix and process them for HDR. Then I would clean up everything in Photoshop with layers. I did a little tutorial here that might help with this....if you are not using Photomatix (you don't need to), you can ignore the photomatix step and go right to the Photoshop step, which starts around 12:20...I was using Elements in this tutorial.
This tutorial is largely all about layer masking, which is how you would get the desired effect on your photo...
But the Photomatix step is not really necessary. You don't have to tonemap this, and when I do this, I definitely don't shoot for a tonemapped look. I try to make it look as natural as I can. The advantage of Photomatix is that it will do a lot of the grunt work of getting your photo properly exposed in all areas. But you can do this manually without Photomatix in Photoshop. In your photo, there's a definite divide between the underexposed and overexposed parts. You could literally paint in what you want.
Let's say that the 3 bracketed exposures are not giving the effect that you want on the waterfall. Then I would take a 4th shot of just the waterfall (keep your tripod steady), and slow down the shutter enough to get the water with whatever effect was desired. Probably go to TV mode, and set to however many seconds it takes to get the effect. Check ISO's to make sure that they didn't change real significantly. If they did, then I'd take a note of the shutterspeed that I needed, and adjust everything else properly in manual mode. As long as this shot is somewhere around the same exposure as the rocks behind the waterfalls, which is should be, no problem. Even if it's not, you could adjust the exposure in Photoshop, or adjust the opacity of the layer.
Then I would include this 4th shot to layer in the waterfall.
I hope that you don't mind, but went ahead and played with your photo. Keep in mind that obviously, I'm doing this without bracketed photos, just your single exposure. If I had bracketed exposures, this would look a lot better. Basically, I raised the exposure on the darkest parts and lowered the exposures on the brightest areas and painted them in. Some of the darkest parts are still pretty dark. Without a bracketed shot, it would create a lot of noise, and ugliness, so I could only push it so far. Like I said, it's not great, it's not even with a RAW file, but it demonstrates the point.
Let me know if this helps.