Autopano pro/ giga usually does a much better job in such situations.
Now, the real trick is to time captured better, but even that rarely works perfectly. :-)
Long exposures obviously always work, but that is a very different look.
If such images are important to you then nothings beats a 6x17 film camera + drum/Imacon scan. Less detail/more grain but perfect results garanteed!
Cheers,
Bernard