Admittedly, I very rarely encounter problems like this in the sky when merging for HDR.
How long were your exposures? It just seems like there was an awful lot of cloud movement while you were taking your bracketed shots. Or were the clouds really moving that fast? Ordinarily, even at f/22, three bracketed exposures of a relatively bright day shouldn't take more than a second or so in total...maybe two or three seconds tops depending on the breadth of dynamic range you need to capture. For that amount of cloud movement to be occurring, there would have to be some pretty serious wind in the atmosphere.
Were you shooting with a filter? If cloud movement is an issue in a scene you're photographing, definitely lose any polarizers or grad nds (though even with these, I've almost never had such a problem with drastic cloud movement).
I would agree with Steve01 that you're best off trying to get Photomatix to remove the ghosting. But, in this case, the change in shape and location of the clouds is so drastic that Photomatix is liable to interpret them as distinct shapes rather ghosts.
Alternatively, you can try scrapping the exposure which is causing most of the ghosting and merging the faster neutral and underexposed shots. You can then try to simply boost fill light in post. You'll certainly generate more noise that way, and the result probably won't be as nice... but you might be able to avoid the ghosting.
Also, you could pull the result into Photoshop as posted and just try to work at it on the pixel level to remove the ghosting. Not sure how well this would work out, but it's worth a couple minutes of experimentation on a small section to see if success is possible.