MySQL InnoDB transactions with lot of delete instructions
this file ibdata1 also known as system tablespace, which consistent of undo log even if you have seperated tables into different files;

from your process I found it is a really huge transaction, which will produce drampatic quantitiy of undo logs, till MySQL 5.5, undo log space can not be shrink or adjust automatically or manually.

so there is a simple way to prevent you from the huge undo log:

commit your transaction every 300 delete statements. 

each next transaction will recycle the undo log space.