Is the fee that you charge the customers a fee to transfer out of their existing account into one at the other institution? Or are you talking about a fee to set up an ACH business customer to send payroll to the other institution? If the second is the case, then it is not the same fee. Those getting receiving the payroll $ don't get charged, the payors do. I'd argue against it.
Regulation E - the commentary:
Paragraph 10(e)(2) —Employment or Government Benefit
1. Payroll. An employer (including a financial institution) may not require its employees to receive their salary by direct deposit to any particular institution. An employer may require direct deposit of salary by electronic means if employees are allowed to choose the institution that will receive the direct deposit. Alternatively, an employer may give employees the choice of having their salary deposited at a particular institution (designated by the employer) or receiving their salary by another means, such as by check or cash.