Last year I added functionality to Chris O'Brien's SharePoint Content Deployment Wizard to copy documents from one library to another. I'm pretty sure I tested that versioning copied over as well.
Have a try of that and if you have any problems using it please leave me a comment here and I'll update my answer with more info.
New Link : https://github.com/chrisdee/Tools/tree/master/SharePoint/SharePointContentDeploymentWizard