SCP, maybe (see below). See Section 6.10(5) of the EPCRS (Rev Proc 2006-27) for overcontributions. Correction under this section generally requires the participant's consent (for trustee or custodia) to have funds disgorged (adj. for earning) from IRA. It might also be possible to leave the funds in the IRAs and pay a fee (10%) under section 6.10(6) and loose the deduction as well for the excess elective contributions.
The employer will have to determine which of the two possible EPCRS approaches is better and whether the fix would be any better if Code provisions alone (a third approach) were used to correct the failure. Legal fees aside, the third approach would probably be more costly, especially if several years are involved.
As one practitioner put it, conflicting and interrelated correction methods have to be resolved to find the fix that best serves the needs of the employer.
The facts presented do not seem to indicate that the failure was egregious (see Section 4.11), however, SCP is only available for a SEP if the failure was insignificant (see Sections 4.01, 8.01). See Section 8 "factors" to determine whether the failure was insignificant.
See EPCRS:
EPCRS - Rev. Proc. 2006-27