Using the freedom of movement act, will we be able to work in EU countries?
Using freedom of movement, you and your wife can live and work in any EU nation other than your own. If you become an Irish citizen, you can no longer rely on Freedom of Movement to live and work in Ireland with your wife.
I recommend that, for the moment, you do not apply for Irish citizenship. The visa process for the spouse of an Irish national requires more evidence than the process for the spouse of an EEA national.
If you wished, you could move to Ireland tomorrow, and your wife could immediately join you. If you are concerned about her entry ban, then she can apply for a visa as the spouse of an EU national resident in Ireland. This cannot be denied on the basis of her overstay in the UK. Ireland is required to issue her this visa under EU law.
Furthermore, once you have moved to Ireland, you may be able to return to the UK under the Surinder Singh route. This would mean that you could return to the UK under freedom of movement law, avoiding the financial requirements of the UK spouse visa. However, it's unknown at this point how this route will be affected by Brexit, and it can also be legally difficult to execute. If you wish to attempt this, you should seek legal advice from a solicitor with experience of the Surinder Singh route.
Our top priority is still to continue our lives in the UK, I recently read that the re-entry ban does not apply to spousal visa applications, is this accurate? Would she need to apply for the spousal visa from South Africa?
As I said on Travel, I believe the entry ban is unlikely to affect your wife, since bans do not apply to spouse visa applications unless there are "aggravating circumstances, such as absconding, not meeting temporary admission/reporting restrictions or bail conditions, using an assumed identity or multiple identities, switching nationality, making frivolous applications or not complying with the re-documentation process", per the immigration rules. For best chances in your spouse visa application, you should seek legal advice on her entry ban.
I recently read that the re-entry ban does not apply to spousal visa applications, is this accurate? Would she need to apply for the spousal visa from South Africa?
She needs to apply for the visa from wherever she is currently resident. She will not be able to apply from within the UK. She could apply from Ireland if she were resident there.