I would set up the SSIS package to insert into a staging table first. Then use a SQL task to check for references in the staging table that does not yet exist, and insert the references. Use something like a left outer join check:

insert into reference_table (reference_id, reference_description)

select s.reference_id, 'some description'

from staging_table s

left join reference_table r on r.reference_id = s.reference_id

where r.reference_id is null

After the references are resolved, copy from the staging table to the actual table being loaded.