The answer is "Yes" - the CAF125 is a deferment (pre-tax) of the employee's wage and should already be subtracted from the total amount reported in Box 1 of the W-2.
The CAF125 entry in Box 14 does not change the way the return is prepared and/or filed.
See What Is "Cafe 125" on a W-2 Tax Form? for a more detailed description of this entry.
