Thanks for your suggestion, we will consider offering such an option, or pay more fees for smaller payouts.
By the way, sending transactions with 0.0001 BTC fee no longer guarantees that it will confirm fast. You can still wait an hour or two during busy hours.
For this reason the fee that we pay depends on how busy the network is and the payout amount. We pay much more than 0.0001 BTC in fees for payouts bigger than 0.33 BTC during busy hours so that you get it confirmed instantly. In some cases we pay 1 mBTC or more.
Maybe you guys should be default pay 0.0001 for any amount between 0 and 1 BTC, and charge the amount from the bet the user places. If someone places a bet of 0.001 at 1.1 odds, then that in anyways in not an intelligent way to bet. You could just have the rule of taking the txn fees of 0.0001 irrespective of the bet sizing.
Thats what most of the other gambling sites do.