SQL Server integration services is designed specifically to do this.
it is primarily used for data warehousing where data is taken from one (or mulitple ) database and stored in another, differently designed database.
in the case of data warehousing the second database is normally designed for better data retrieval and reporting access and less concerned with normalisation.
often this process will use an intermediary to allow for multi stage transformation
this process is often called ETL (Extract transform and Load)