This would only involve your employer if your employer requested the return of contribution be paid to them, in which case, if the amount contributed through the employer was by payroll deduction, the employer would pay you the money refunded to them and include it in box 1 of your W-2, withholding accordingly. If you obtain the distribution yourself, you would not involve your employer and, when you enter the code 2 Form 1099-SA for a return of excess contribution, TurboTax will automatically include the amount in income, including whatever amount the HSA custodian calculates and distributed as the earnings on the excess contribution, reported in box 2 of the Form 1099-SA.
The calculation is the same as for a return of contribution from an IRA before the due date of your tax return. The HSA custodian should do the calculation for you when you tell them that you want a return of excess contribution. CFR 1.408-11 describes the required calculation: https://www.law.cornell.edu/cfr/text/26/1.408-11
