Once beta is passed with the current design, we plan on adding a feature to allow users to pay the fee via Lightning.
How is the fee paid at the moment? Is it simply as an additional output from the withdrawal transactions? If so, this raises significant privacy concerns as not only will the fees be of common values since both the fee rate and the standard statecoin sizes are static, but you will then have to consolidate all these fees together in to your own wallets, which again will aid in identifying them as coming from Mercury, and therefore identify the coins which were withdrawn as having come from Mercury.
What about a way for a user to pre-pay 10/20/50 whatever withdrawals in advance, much like TrustedCoin do for 2FA Electrum wallets? Both a privacy benefit for the user and a financial benefit for you for not having to consolidate so many small outputs.