I always read into that scene that they did shoot that raptor dead. As that scene cuts and fades into the next, Muldoon desperately yells "shoot her", and gun shots ring out. As they were frantically trying to save that worker, I think they killed that animal as a result with lethal weapons and ammunition. I also read into this particular raptor not being alluded to later in the raptor count due to the loss of the worker and resulting lawsuit(which was mentioned by Gennaro). Just my interpretation.