I don't think the bank account will be a large issue. It is possible and legal to run a schedule C business using only a single business/personal account, although that certainly makes bookkeeping more difficult, and I would always recommend having separate business and personal bank accounts and credit cards whenever possible.
If this is a one-shot, transfer the money into your personal account and forget about it. The IRS probably won't come looking and if they do, show them the proof this was a clerical error. If your wife might have more contracts in the future, or to clean up the bookkeeping on this one, open an account in her own name with either an EIN or her SSN and transfer the money.
