There is no 10% penalty on the earnings distributed with a distribution of an excess deferral or excess Roth contribution from an account in a 401(k) plan.
Particularly since the corresponding tax year has not yet ended. the request to make the distribution of the excess should be done through the employer; the employer is likely the administrator of the plan. As Critter-3 indicated, this will allow the employer to produce a W-2 that reflects the net contribution. You should indicate that the excess adjusted for gain or loss should be distributed from the Roth 401(k) account even though, I think, that the excess is deemed to be in the Roth 401(k) account and should come from that account anyway.
