TW,
On a direct flight back from the Bahamas, a DL should work fine with the US INS. It is much the same as arriving from Canada.
However, I am certainly in AC*SE's camp when it comes to passports. They are the best form of ID for a US citizen abroad, and can be replaced by local embassies and consulates around the world if lost or stolen, unlike DL's.
You state that 'She has begun the process to have it replaced.' If she is still in the document-collecting phase, and has not yet applied for a new passport, she might want to consider going over to the nearest Passport Agency (such as the one in Miami assuming that is the closest agency), and paying a slight surcharge to get a passport issued in several within a day. That usually requires proof of an imminent overseas trip, such as tickets or airline-generated itinerary. She will still have to file a form for a lost passport.
I know that the Philadelphia Passport Agency does 3-hour turnarounds, but I'm not 100% sure about Miami. You can contact them at:
MIAMI Passport Agency
Claude Pepper Federal Office Building
51 SW First Avenue
3rd Floor
Miami, FL 33130-1680
Hours: 8:30 a.m. - 3:30 p.m., local time, M-F, excluding Federal holidays
Automated Appointment Number: (305) 539-3600