Yipes! This is a complicated situation for sure.

I am not an attorney, nor an immigration specialist, so I cannot offer you official advice. However, I would think that your boyfriend has to figure out some way to sort out his situation with overstaying his UK residence permit before you do anything else. Is he working with a solicitor or the embassy? If not, I would definitely suggest that he do so, right away.

As for marriage, it depends. Do you want to live in South Africa or in the UK? If you want to live in South Africa, it might be easier for you to get married before you go, since you would be able to apply for residency as a spouse rather than as a partner or fiancee. If you want to live in the UK, it might be easier for you to get married where you are once your boyfriend's divorce is sorted out. Since you are (I assume) living in the UK legally, it might help him to obtain a residency permit as well.

If he has to leave the UK, then you might consider going with him, getting married in South Africa, and then returning. You might be able to return together, but he might have to stay behind until he gets his immigration status sorted. Not the best situation, but if you truly love one another, it will definitely be easier for him to obtain a residence permit as a spouse of a legal resident. So getting married will probably help in that respect.

As I said, this is all just my own speculation -- PLEASE consult with an attorney and with the South African and UK embassies before you take any further action.