I'll be coming later in the year, so if worst case, we can apply for her passport same day of the event, she flies to Brasil using her Brazilian passport, and then I bring the US Passport so she can re-enter the USA.
Interesting enough, the US embassy in Dominican Republic actually mentions this scenario of only traveling with the certificate of naturalization:
https://do.usembassy.gov/do-not-travel-without-us-passport/