Sorry about my misinterpretation. I'm sure her payroll dept will know how to do this.
In simple terms, if your wife was paid 1,500 gross pay in error, the payroll calculated tax and other deductions on this basis. If they put through -1,500 (minus 1,500), refunds of tax and other deductions will be calculated, leaving her gross and net pay pretty much where they would have been if the erroneous payment had not been made. Any minor adjustments will be picked up when they reactivate her on the payroll when she returns after maternity leave.
I believe her employer will need her written permission to make the one-off deduction from her pay and your wife will need to agree to pay back the overpaid net pay. This can be once-off or over a number of months as suits her circumstances. AFAIK they cannot force her to make a single payment.