That's what the Price Margin percentage is for. Which reminds me: it would be nice to be able to sort a column by clicking it's header.
Too often, I have seen discrepancies when something is expressed in percentages.
What are the possible solutions to this? Can't you change the type of currency to get the service fee to a blockchain where such issue won't occur? Or can't you make multiple transactions to the same buffer wallet and when it will have enough satoshi from all the dust left by all the other trades, you could move them?
Probably the best solution is to set a minimum fixed fee, for example, 0.000005 BTC per transaction