For example, if the user adds $100 to his ETH account and only withdraws $70, after a $20 commission, he is left with $10 on his account that he will never get to use.
Your commission or miner's commission? The latter can't be tackled somehow. Ethereum doesn't seem to scale with these fees and if you want to protect your customers about this situation you need to warn them before every withdrawal.
For instance, if they have $100 in ETH and want to withdraw $70, you can recommend them to withdraw $80 instead and empty their balance instead of leaving a temporarily unspendable amount of $10.