About the Navy, that's a good question. We heard about the "coasties" who, according to Kimmet's recap "pulled their shit togheter faster than anyone". That's not the Navy, I suppose? Because I understood from Kimmet's recap that they were decimated while trying to use non lethal force in the hope to find a cure.
As for CJ, she's dead, that's it. I don't think there's anything to discuss, we hear the flesh being cut when the knife is pulled out of the would. And unless somebody arrives IMMEDIATELY with a firearm, somebody who arrived with Saul but stayed conveniently back by exactly the amount of steps necessary for Scratch to kill CJ before his or her arrival, Saul is dead too. Scratch bested Durai, CJ, who knows who else, and Saul is just an half conscious hurt man on the floor (tiles, rugs, whatever :P)

As for the satphone: the only scenario I can think of in which Scratch is calling Irwin is:
- Lizzy and Victor get to the hospital;
- Scratch dodges bullets, blades and shurikens thrown her way 'cause she's immortal;
- gets close to Lizzy and takes her hostage.
- using the leverage provided by a pregnant hostage she finds what they were up to and forces Glenn to fix the phone.
Now, as for why would she want to call an active military base and potentially attract helicopters, tanks and B52 bomber on herself, I have no clue. But then again, she's immortal, so why should she care, right?