You are going to have to get in touch with HMRC one way or another. The best time to get them on the phone is at 8am each morning including Saturdays. The contact details are here
When you get through, ask HMRC to issue a P810 which is a form sometimes sent to taxpayers not in self-assessment for them to disclose income. I agree that it would seem to be pointless to have your wife put into the SA system for a period of 3 months but HMRC may insist.
You could ask HMRC them if they would include the £3,000 as a restriction in your wife's current tax code so as to collect the tax that way but given the size of the payment, they may not agree to do that. In any event, that may cause her to pay too much tax given the size of her salary.
As the locum period was a one-off period of self-employment, HMRC may only need one tax return to be completed. You can make it clear in the return that tax returns for future years will not be needed.
I'm afraid that there is no easy way through this for you. If you write a letter, you could wait for two months or more for a reply.
I hope this helps but let me know if you have any further questions.