I'm afraid that her situation is not as simple as you think, I regret to say.
In order for a person to be eligible for naturalisation as a UK citizen.You can see it on this page ("Immigration Time Restrictions"):-
This means that a person wishing to apply must have first obtained indefinite leave to remain. If your wife does not presently have this then there is no possibility of a successful application.
Furthermore, he situation is complicated by the fact that her current visa has expired. If she had attained 5 continuous years in that category then she could apply for ILR. Because it expired more than 28 days ago she is technically classed as an overstayer. She should have made an application to extend it or to switch in to a spouse visa category before it expired I'm afrad.
The quicker possible way for her to now obtain ILR would be to complete two years in a spouse visa category. Overstays are not grounds for refusal in the case of marriage applications.
She can attempt to do this by making an application in country for a spouses visa by using form FLR(M) but the UKBA come down on overstayers like a ton of bricks and the likelihood is that they will say that she needs to return to SA and make an application from there by Form VAF4. They only permit overstayers.to make in courty applications in exceptional circumstances (ie. where to not do would prejudicially affect the health of the applicant or their family)
I'm very sorry it could not be better news.
I hope this helps, if so please kindly click accept so that I may be rewarded for my time. It will be gratefully received and you will be free to ask follow up questions.