How can my wife convert her 90-day tourist visa to a Non-O spousal visa after arriving in Thailand?

You need to talk to your employer first if they agree to support your wife's visa. While she could apply for an in-country Non-O trailing spouse to a foreigner who is working in Thailand legally, she needs a bunch of documents from your employer for her to be able to apply. Without them, she cannot apply for Non-O on her own.

You have to be on 1-year extension based on employment before she can apply for her Non-O.

Also, you need to be careful if she gets SETV from Pretoria. A while ago, Pretoria used to put a note onto the visa saying the visa holder HAS TO return to SA to apply for another visa (Not many reports after Covid chaos though). If this note is on her visa, she has no choice other than to go back to SA to apply for her Non-O.