I didn't find any information about variables in control file in the docs. However, given that you're running the whole thing from
Java, you could easily create the control file for each run and stuff the required table name into it.
If your program can access to a file system your database server can see, you could also consider external tables. Generally, anything that can be processed using SQL Loader can be processed by external tables. The "loading" is then done using a SQL command (insert into your_target_table as select from external_table) which would clearly be fully under your control.