I thought she was in complete shock after the rebellion was apparently wiped out, yeah, especially since she admired the coalition-building so much and had repeatedly tried to save them, and they had helped her. Without Ash, without the idea of the Federation somehow surviving even in this verse, and without Saru and the rest of her crew, she's really ungrounded. PLUS, then her mentor and the woman who basically symbolizes Starfleet in the show is the supreme evil leader? BSOD for sure.

(Lorca didn't bow either, heh.)