This must be a Canada thing. Neither my bank nor my employer charge anything for direct deposit. In fact, the bank waves certain online banking fees if you have direct deposit (or a balance over a certain amount). I can either split the deposit before it leaves my employer (up to three different accounts) or once it hits the bank.
If your bank is charging for this, find another bank. <img src="/images/graemlins/smile.gif" alt="" />