What should I do if I need to leave Thailand due to a family emergency while waiting for my marriage visa extension?

If extension of the under consideration is not agreeable for immigration you can just get re-entry permit and travel.

It’s ok as long as you return by September 3rd and make your appointment.

Or if you stay longer then apply non-O visa from your home country and apply the annual extension again once back.

The under consideration period can be extended, its discretion and immigration are likely to be sympathetic to your circumstances, but as Tod says take your Thai wife.

So now you're on an under consideration stamp and report back on Sept 3 to get that year extension inked in?

All you can do is go (with your thai wife) to your immigration office and see if they can either expedite the under consideration (unlikely) OR if they can give you more time on the under consideration stamp (i have seen this happen)

Other than that, if you have to leave the country before you "close the loop" (get the year extension inked in) you'd lose this application and when you come back you'd have to start all over with a new Non-O and then a year extension.