The way I interpret that is she was at the Temple entrance, most likely, and just fled when Vader and the 501st Legion arrived. Perhaps she didn't have the chance to save the younglings then. If that's the case, I don't believe it was cowardice, but it does leave a bad taste in my mouth nonetheless.
I wonder why Vader couldn't off Shaak-Ti right there? How did she get past Vader and the 501st Legion?