"Nephilim," IMO, means hybrid fallen angel/human offspring. Maybe the giant the SOG killed was just a natural mutation - or not?
I do believe "those in Christ" will be called up to join Him at some point. I'm not sure at what point that will be, but think it is before the actual "Day of the Lord" or just before the "real" fireworks begin.
Then there are other protections mentioned in scripture, such as when the angel marks the dwellings of the righteous, which coincides with the prophetic warning of Isaiah to go inside your home and shut the door until everything passes.