There are two ways to do this that I can think of. One of them is the to change Style's TargetType in our Generic.xaml which you want to avoid. Note that we are making changes to our theming mechanism and optimizing it. So in a week for the SP1 there will be some changes and is also expected the size of the Generic.xaml to be significantly decreased.
The other way is to set specifically Vista theme in the constructor of each control and point to where your resources are. This will allow the proper theme to be set when the control is loaded.
I would advise you to wait for SP1 and see what the changes are and maybe it won't be that much work to modify the Generic.xaml then.
the Telerik team