Did you tried to pass the tgt_delete_flag column in your file for the relationships too?
the value to be pass there are: active/inactive
Will need to do a small test but I don't think there is any limitation there.
You will only be able to set those as inactive via this method but must work.
Load data using Web Services into the TWA table then use GRloader command to commit the data to the CMDB or either use GRLoader directly for both.
You can also eventually extend (with small mod/spl customization) to Call GRloader directly from Web services.
Hope this help
/J