Entering a 1099-R with excess/earnings as you suggest, will get the income taxed, but won't remove the overcontribution error from your W-2s and penalty assessment.
Otherwise, you could change the Box 12 amount on one of your W-2s (but still need to report excess/earnings as 'Other Income') to account for the changed W-2 but get rid of the TurboTax overcontribution error.
If you do this, you may want to make two 'Other Income' entries; one for 'excess deferral' (to account for Box 12 change) and one for 'earnings on excess deferral', then ignore the the 1099-Rs you receive later.
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