At the moment I see only one option: in the Data Flow Source the Access Mode can be set to "SQL command" instead of "Table", and with Sql Command like "select * from table..." it does not return deleted records.

This is what I have found at http://forums.microsoft.com/MSDN/ShowPost.aspx?PostID=226606&SiteID=1 :

"....using table access always returns the deleted records as well. Presumably this is because you might be moving them to another FoxPro database, which can distinguish the deleted from the real."

Do not know whether it is "official" though.