If the plan’s administrator (or other responsible plan fiduciary) had approved the service provider’s distribution-processing fee (including for plan-termination distributions), applying the approved fee might be a reasoned method.
Think carefully about what the resulting Form 1099-R tax-information report will look like.
Will the trustee’s, custodian’s, or other payer’s software generate a 1099-R report if a distribution’s amount is $0.00?
Think about how the plan’s administrator (usually, the employer) will make and keep evidence that each zeroed-out distributee was paid all that was due her.
This is not advice to anyone.