However, it's 2068 in this story, and the carrier group is already well on its way to NC (it does not take two years for a carrier group to cross the Pacific. Even real life carriers are shockingly fast). Probably because Taylor's presence, public profile, and family connections allowed Rhyne to use her as a covert communications back channel that would not have otherwise been available to him.
As for the cruise missile strike, I can't be sure. My guess is that it's petty retaliation by the NUSA after failing to stop Arasaka's arrival. They must've realized that Arasaka is en route due to an invitation. It's also possible that President Myers ordered the NUSA forces in NC to do something in addition to the missile strikes, but their commander (Hansen), can see the writing on the wall and simply disobeyed.
