You should probably just eat the fee or increase your other fees to compensate for the fees. You should
not charge users for the fees caused by their withdrawals because the actual fee depends on transactions that
other users are making. If someone funds their account with 100 transactions adding up to 0.2 BTC, the large number of transactions will increase fees for everyone. That transaction you referenced is expensive due to this kind of wallet fragmentation, not because the transaction's value is large.
I have my fees set to 0.0001 BTC for my customers in the bitcoin.conf file
That's unnecessary. Bitcoin-Qt will never use a too-low fee. Even if you set your fee to 0, you will pay fees.