Hi Natalia,
maybe you have already saved your problem?!
We were just facing the same one and found a very simple solution. Instead of populating data to a Z-Table we just defined a view in the ABAP dictionary of the ERP system which includes the filtering for the relevant rows and columns of the source table (in our case HRP1001 which is even bigger).
Instead of entering HRP1001 as value to parameter TABLE we added the name of the view then (e. g. ZHRP1001).
This does not involve any BAdI or triggers to populate data into other tables and is completely transparent to the IDM.
We had just to add some authorizations to the RFC user (S_TABU_NAM and S_TABU_DIS), which were very restrictive before, and reduced our load time from about 2,5 hours to less than 10 seconds (memory usage has been reduced also dramatically).
Maybe this hint is helpful for others or even for you if you did not yet find a good solution for your problem.
Regards,
Dirk