The excess contribution "penalty" is actually an excise tax. If changing your filing status to MFJ made you eligible to make the Roth IRA contribution, you are no longer subject to the excess-contribution excise tax and your amendment changing your tax return to MFJ should have reflected that by including a correction to your originally filed Form 5329, resulting in a change on the Other taxes line of Form 1040X. If your previous amendment did not include the corrected Form 5329 and the corresponding change on the Other taxes line of Form 1040X, amend again to make the change and to receive a refund of the excise tax.
Had you used TurboTax to amend a MFS tax return to MFJ, TurboTax should have included the corresponding change on the Other taxes line of Form 1040X. However, because Form 5329 Part IV became all zeros, TurboTax probably would have omitted this form. To explicitly indicate that you are no longer subject to the excess-contribution tax, your amendment should include Form 5329 Part IV with the previous non-zero amounts zeroed.
