This is a simple enough task to do in model builder -- the kind of stuff it's really good at, no user input, or error checking, just run the tools and be done with it.
Seems to me the best approach would be not to recreate the feature classes from scratch, but run the delete rows tool on each of your feature classes and then use the Append tool to copy new data into those feature classes. This would avoid having to regenerate indexes, relates, or domain settings.
If you have a model builder model that works, all the python script has to do is create a geoprocessor, add your toolbox that contains your model, and run the tool.