The Metadata Toolset will allow you to import metadata from the source feature class into the destination feature class... However, you will only retain metadata from one of the input feature classes, not both: Merging metadata stylesheets does not work with ArcGIS - exporting each input feature class metadata to a template and merging both templates will actually results in overwriting one by the other, not merging contents.
You would need to use an external XSL transformation tool to manipulate your metadata XML files, and import the results into your destination feature class. My office implemented a workflow apparently close to yours using Saxon Home-Edition. XSL scripting is hard to learn, however.