Let me first say that being able to take 17 million records from a flat file, pushing to a DB on a remote box and having it take 7 minutes is amazing. SSIS truly is fantasti
Use the Sort Component.
Simply choose which fields you wish to sort your loaded rows by and in the bottom left corner you'll see a check box to remove duplicates. This box removes any rows which are duplicates based on the sort criteria only so in the example below the rows would be considered duplicate if we only sorted on the first field:
1 | sample A |
1 | sample B |